WorldWideScience

Sample records for source molecular workbench

  1. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  2. A Flexible Electronics Laboratory with Local and Remote Workbenches in a Grid

    Directory of Open Access Journals (Sweden)

    Thomas Lagö

    2008-05-01

    Full Text Available The Signal Processing Department (ASB at Blekinge Institute of Technology (BTH has created two online lab workbenches; one for electrical experiments and one for mechanical vibration experiments, mimicking and supplementing workbenches in traditional laboratories. For several years now, the workbenches have been used concurrently with on-site ones in regular, supervised lab sessions. The students are encouraged to use them on a 24/7 basis for example, in preparation for supervised sessions. The electronic workbench can be used simultaneously by many students. The aim of a project known as VISIR (Virtual Systems in Reality founded by ASB at the end of 2006, is to disseminate the online lab workbenches using open source technologies. The goal is to create a template for a grid laboratory where the nodes are workbenches for electrical experiments, located at different universities. This paper focuses on standards, pedagogical aspects, and measurement procedure requirements.

  3. Analyst workbenches state of the art report

    CERN Document Server

    Rock-Evans, R

    1987-01-01

    Analyst Workbenches examines various aspects of analyst workbenches and the tasks and data that they should support. The major advances and state of the art in analyst workbenches are discussed. A comprehensive list of the available analyst workbenches, both the experimental and the commercial products, is provided. Comprised of three parts, this book begins by describing International Computers Ltd's approach to automating analysis and design. It then explains what business analysis really means, outlines the principal features of analyst workbenches, and considers the ways in which they can

  4. Data analysis workbench

    International Nuclear Information System (INIS)

    Goetz, A.; Gerring, M.; Svensson, O.; Brockhauser, S.

    2012-01-01

    Data Analysis Workbench (DAWB) is a new software tool being developed at the ESRF. Its goal is to provide a tool for both online data analysis which can be used on the beamlines and for offline data analysis which users can use during experiments or take home. The tool includes support for data visualization and work-flows. work-flows allow algorithms which exploit parallel architectures to be designed from existing high level modules for data analysis in combination with data collection. The workbench uses Passerelle as the work-flow engine and EDNA plug-ins for data analysis. Actors talking to Tango are used for sending commands to a limited set of hardware to start existing data collection algorithms. A Tango server allows work-flows to be executed from existing applications. There are scripting interfaces to Python, Javascript and SPEC. The current state at the ESRF is the workbench is in test on a selected number of beamlines. (authors)

  5. The DCR Workbench: Declarative Choreographies for Collaborative Processes

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas

    2017-01-01

    analysis, time analysis, enforcement, declarative subprocesses, data dependencies, translation to other declarative models, and more. This chapter introduces the Workbench and, through the features of the Workbench, surveys the DCR formalism. The Workbench is available on-line at http: //dcr.tools....

  6. Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.

    Science.gov (United States)

    Pérez-Rodríguez, Gael; Glez-Peña, Daniel; Azevedo, Nuno F; Pereira, Maria Olívia; Fdez-Riverola, Florentino; Lourenço, Anália

    2015-03-01

    Biofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. The workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. First, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. A considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at http://sing.ei.uvigo.es/bew under LGPL license. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. Integration of Dakota into the NEAMS Workbench

    Energy Technology Data Exchange (ETDEWEB)

    Swiler, Laura Painton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lefebvre, Robert A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Langley, Brandon R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thompson, Adam B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-07-01

    This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on integrating Dakota into the NEAMS Workbench. The NEAMS Workbench, developed at Oak Ridge National Laboratory, is a new software framework that provides a graphical user interface, input file creation, parsing, validation, job execution, workflow management, and output processing for a variety of nuclear codes. Dakota is a tool developed at Sandia National Laboratories that provides a suite of uncertainty quantification and optimization algorithms. Providing Dakota within the NEAMS Workbench allows users of nuclear simulation codes to perform uncertainty and optimization studies on their nuclear codes from within a common, integrated environment. Details of the integration and parsing are provided, along with an example of Dakota running a sampling study on the fuels performance code, BISON, from within the NEAMS Workbench.

  8. Using bio.tools to generate and annotate workbench tool descriptions

    DEFF Research Database (Denmark)

    Hillion, Kenzo-Hugo; Kuzmin, Ivan; Khodak, Anton

    2017-01-01

    - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates...

  9. ARC integration into the NEAMS Workbench

    Energy Technology Data Exchange (ETDEWEB)

    Stauff, N. [Argonne National Lab. (ANL), Argonne, IL (United States); Gaughan, N. [Argonne National Lab. (ANL), Argonne, IL (United States); Kim, T. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2017-01-01

    One of the objectives of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Integration Product Line (IPL) is to facilitate the deployment of the high-fidelity codes developed within the program. The Workbench initiative was launched in FY-2017 by the IPL to facilitate the transition from conventional tools to high fidelity tools. The Workbench provides a common user interface for model creation, real-time validation, execution, output processing, and visualization for integrated codes.

  10. Finite element modeling and simulation with ANSYS workbench

    CERN Document Server

    Chen, Xiaolin

    2014-01-01

    IntroductionSome Basic ConceptsAn Example in FEA: Spring SystemOverview of ANSYS WorkbenchSummaryProblemsBars and TrussesIntroductionReview of the 1-D Elasticity TheoryModeling of TrussesFormulation of the Bar ElementExamples with Bar ElementsCase Study with ANSYS WorkbenchSummaryProblemsBeams and FramesIntroductionReview of the Beam TheoryModeling of Beams and FramesFormulation of the Beam ElementExamples with Beam ElementsCase Study with ANSYS WorkbenchSummaryProblemsTwo-Dimensional ElasticityIntroductionReview of 2-D Elasticity TheoryModeling of 2-D Elasticity ProblemsFormulation of the Pla

  11. The Spoofax language workbench

    NARCIS (Netherlands)

    Kats, L.C.L.; Visser, E.

    2010-01-01

    Spoofax is a language workbench for efficient, agile development of textual domain-specific languages with state-of-the-art IDE support. It provides a comprehensive environment that integrates syntax definition, program transformation, code generation, and declarative specification of IDE components

  12. Evaluating the Effects of Interactivity in a Post-Editing Workbench

    DEFF Research Database (Denmark)

    Underwood, Nancy; Mesa-Lao, Bartolomé; Martinez, Mercedes Garcia

    2014-01-01

    This paper describes the field trial and subsequent evaluation of a post-editing workbench which is currently under development in the EU-funded CasMaCat project. Based on user evaluations of the initial prototype of the workbench, this second prototype of the workbench includes a number of inter...... on productivity, quality, user satisfaction and cognitive load as reflected in the post-editors’ gaze activity. These quantitative results are combined with the qualitative results derived from user questionnaires and interviews conducted with all the participants....

  13. Context-Dependent Help for the DynaLearn Modelling and Simulation Workbench

    NARCIS (Netherlands)

    Beek, W.; Bredeweg, B.; Latour, S.; Biswas, G.; Bull, S.; Kay, J.; Mitrovic, A.

    2011-01-01

    We implemented three kinds of context-dependent help for a qualitative modelling and simulation workbench called DynaLearn. We show that it is possible to generate and select assistance knowledge based on the current model, simulation results and workbench state.

  14. The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.

    Science.gov (United States)

    Stocks, Matthew B; Mohorianu, Irina; Beckers, Matthew; Paicu, Claudia; Moxon, Simon; Thody, Joshua; Dalmay, Tamas; Moulton, Vincent

    2018-05-02

    RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs. Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses. The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench. v.moulton@uea.ac.uk.

  15. Low-cost workbench client / server cores for remote experiments in electronics

    OpenAIRE

    José M. M. Ferreira; Americo Dias; Paulo Sousa; Zorica Nedic; Jan Machotka; Ozdemir Gol; Andrew Nafalski

    2010-01-01

    This paper offers an open-source solution to implement low-cost workbenches serving a wide range of remote experiments in electronics. The proposed solution comprises 1) a small (9,65 x 6,1 cm) Linux server board; 2) a server core supporting two TCP/IP communication channels, and general purpose I/O pin drivers to interface the remote experiment hardware; and 3) a client core based on a multi-tab user interface supporting text file management to exchange experiment scripts / status informatio...

  16. Scalable web services for the PSIPRED Protein Analysis Workbench.

    Science.gov (United States)

    Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

    2013-07-01

    Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

  17. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    International Nuclear Information System (INIS)

    Mike Bockelie; Dave Swensen; Martin Denison

    2002-01-01

    This is the fifth Quarterly Technical Report for DOE Cooperative Agreement No: DE-FC26-00NT41047. The goal of the project is to develop and demonstrate a computational workbench for simulating the performance of Vision 21 Power Plant Systems. Within the last quarter, our efforts have become focused on developing an improved workbench for simulating a gasifier based Vision 21 energyplex. To provide for interoperability of models developed under Vision 21 and other DOE programs, discussions have been held with DOE and other organizations developing plant simulator tools to review the possibility of establishing a common software interface or protocol to use when developing component models. A component model that employs the CCA protocol has successfully been interfaced to our CCA enabled workbench. To investigate the software protocol issue, DOE has selected a gasifier based Vision 21 energyplex configuration for use in testing and evaluating the impacts of different software interface methods. A Memo of Understanding with the Cooperative Research Centre for Coal in Sustainable Development (CCSD) in Australia has been completed that will enable collaborative research efforts on gasification issues. Preliminary results have been obtained for a CFD model of a pilot scale, entrained flow gasifier. A paper was presented at the Vision 21 Program Review Meeting at NETL (Morgantown) that summarized our accomplishments for Year One and plans for Year Two and Year Three

  18. Launching an EarthCube Interoperability Workbench for Constructing Workflows and Employing Service Interfaces

    Science.gov (United States)

    Fulker, D. W.; Pearlman, F.; Pearlman, J.; Arctur, D. K.; Signell, R. P.

    2016-12-01

    A major challenge for geoscientists—and a key motivation for the National Science Foundation's EarchCube initiative—is to integrate data across disciplines, as is necessary for complex Earth-system studies such as climate change. The attendant technical and social complexities have led EarthCube participants to devise a system-of-systems architectural concept. Its centerpiece is a (virtual) interoperability workbench, around which a learning community can coalesce, supported in their evolving quests to join data from diverse sources, to synthesize new forms of data depicting Earth phenomena, and to overcome immense obstacles that arise, for example, from mismatched nomenclatures, projections, mesh geometries and spatial-temporal scales. The full architectural concept will require significant time and resources to implement, but this presentation describes a (minimal) starter kit. With a keep-it-simple mantra this workbench starter kit can fulfill the following four objectives: 1) demonstrate the feasibility of an interoperability workbench by mid-2017; 2) showcase scientifically useful examples of cross-domain interoperability, drawn, e.g., from funded EarthCube projects; 3) highlight selected aspects of EarthCube's architectural concept, such as a system of systems (SoS) linked via service interfaces; 4) demonstrate how workflows can be designed and used in a manner that enables sharing, promotes collaboration and fosters learning. The outcome, despite its simplicity, will embody service interfaces sufficient to construct—from extant components—data-integration and data-synthesis workflows involving multiple geoscience domains. Tentatively, the starter kit will build on the Jupyter Notebook web application, augmented with libraries for interfacing current services (at data centers involved in EarthCube's Council of Data Facilities, e.g.) and services developed specifically for EarthCube and spanning most geoscience domains.

  19. AWOB: A Collaborative Workbench for Astronomers

    Science.gov (United States)

    Kim, J. W.; Lemson, G.; Bulatovic, N.; Makarenko, V.; Vogler, A.; Voges, W.; Yao, Y.; Kiefl, R.; Koychev, S.

    2015-09-01

    We present the Astronomers Workbench (AWOB1), a web-based collaboration and publication platform for a scientific project of any size, developed in collaboration between the Max-Planck institutes of Astrophysics (MPA) and Extra-terrestrial Physics (MPE) and the Max-Planck Digital Library (MPDL). AWOB facilitates the collaboration between geographically distributed astronomers working on a common project throughout its whole scientific life cycle. AWOB does so by making it very easy for scientists to set up and manage a collaborative workspace for individual projects, where data can be uploaded and shared. It supports inviting project collaborators, provides wikis, automated mailing lists, calendars and event notification and has a built in chat facility. It allows the definition and tracking of tasks within projects and supports easy creation of e-publications for the dissemination of data and images and other resources that cannot be added to submitted papers. AWOB extends the project concept to larger scale consortia, within which it is possible to manage working groups and sub-projects. The existing AWOB instance has so far been limited to Max-Planck members and their collaborators, but will be opened to the whole astronomical community. AWOB is an open-source project and its source code is available upon request. We intend to extend AWOB's functionality also to other disciplines, and would greatly appreciate contributions from the community.

  20. Using bio.tools to generate and annotate workbench tool descriptions [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Kenzo-Hugo Hillion

    2017-11-01

    Full Text Available Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.

  1. ANSYS workbench tutorial release 14 structural & thermal analysis using the ANSYS workbench release 14 environment

    CERN Document Server

    Lawrence, Kent L

    2012-01-01

    The exercises in ANSYS Workbench Tutorial Release 14 introduce you to effective engineering problem solving through the use of this powerful modeling, simulation and optimization software suite. Topics that are covered include solid modeling, stress analysis, conduction/convection heat transfer, thermal stress, vibration, elastic buckling and geometric/material nonlinearities. It is designed for practicing and student engineers alike and is suitable for use with an organized course of instruction or for self-study. The compact presentation includes just over 100 end-of-chapter problems covering all aspects of the tutorials.

  2. Designers workbench: toward real-time immersive modeling

    Science.gov (United States)

    Kuester, Falko; Duchaineau, Mark A.; Hamann, Bernd; Joy, Kenneth I.; Ma, Kwan-Liu

    2000-05-01

    This paper introduces the Designers Workbench, a semi- immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing, and computer-aided engineering systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates form a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The Designers Workbench aims at closing this technology or 'digital gap' experienced by design and CAD engineers by transforming the classical design paradigm into its fully integrate digital and virtual analog allowing collaborative development in a semi- immersive virtual environment. This project emphasizes two key components form the classical product design cycle: freeform modeling and analysis. In the freedom modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.

  3. ANUSpect-workbench for nuclear spectroscopy

    International Nuclear Information System (INIS)

    Padmini, S.; Diwakar, M.P.; Mukhopadhyay, P.K.; Pande, S.S.; Kataria, S.K.

    2001-01-01

    Multi-channel analyzers (MCA) are used extensively in nuclear instrumentation for research in physics, radiochemistry and many other branches of science. Though large variety of MCA hardware cards and analysis software packages are available, due to incompatibilities, user cannot mix and match these as per his requirement. Here, we present the components based approach used in the design of ANUSpect workbench, so as to give the user liberty in selecting the acquisition hardware and the analysis software for gamma, X ray and alpha spectrum analysis. AnuSpect will work under different MS Windows platforms. The paper also highlights the main functional features and the present implementation status. (author)

  4. Advanced circuit simulation using Multisim workbench

    CERN Document Server

    Báez-López, David; Cervantes-Villagómez, Ofelia Delfina

    2012-01-01

    Multisim is now the de facto standard for circuit simulation. It is a SPICE-based circuit simulator which combines analog, discrete-time, and mixed-mode circuits. In addition, it is the only simulator which incorporates microcontroller simulation in the same environment. It also includes a tool for printed circuit board design.Advanced Circuit Simulation Using Multisim Workbench is a companion book to Circuit Analysis Using Multisim, published by Morgan & Claypool in 2011. This new book covers advanced analyses and the creation of models and subcircuits. It also includes coverage of transmissi

  5. The portability of the "Electronics Workbench" simulation software to China

    NARCIS (Netherlands)

    Collis, Betty; Zhi-Cheng, Dong

    1993-01-01

    This article discusses the portability of the Canadian-made simulation software package, "Electronic Workbench" package (EWB) to China. As part of a larger project investigating the portability of various educational software packages, the EWB package was used in electronics instruction in China and

  6. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    Directory of Open Access Journals (Sweden)

    Carol A Soderlund

    Full Text Available Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor, where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense, and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available

  7. Assessment of the Usability of the Workbench Faraday Cage Method

    DEFF Research Database (Denmark)

    Sørensen, Morten; Franek, Ondrej; Christensen, Søren K.

    2011-01-01

    The workbench Faraday Cage method (WBFC) is a time efficient module pre-compliance test regarding radiated emission. This work investigates the method’s usability and credibility and concludes that for this particular case the WBFC perform a tolerable compliance test for frequencies below 360 MHz...

  8. The Artemis workbench for system-level performance evaluation of embedded systems

    NARCIS (Netherlands)

    Pimentel, A.D.

    2008-01-01

    In this paper, we present an overview of the Artemis workbench, which provides modelling and simulation methods and tools for efficient performance evaluation and exploration of heterogeneous embedded multimedia systems. More specifically, we describe the Artemis system-level modelling methodology,

  9. E-HOSPITAL - A Digital Workbench for Hospital Operations and Services Planning Using Information Technology and Algebraic Languages.

    Science.gov (United States)

    Gartner, Daniel; Padman, Rema

    2017-01-01

    In this paper, we describe the development of a unified framework and a digital workbench for the strategic, tactical and operational hospital management plan driven by information technology and analytics. The workbench can be used not only by multiple stakeholders in the healthcare delivery setting, but also for pedagogical purposes on topics such as healthcare analytics, services management, and information systems. This tool combines the three classical hierarchical decision-making levels in one integrated environment. At each level, several decision problems can be chosen. Extensions of mathematical models from the literature are presented and incorporated into the digital platform. In a case study using real-world data, we demonstrate how we used the workbench to inform strategic capacity planning decisions in a multi-hospital, multi-stakeholder setting in the United Kingdom.

  10. A web-based virtual laboratory workbench for electrical circuits with ...

    African Journals Online (AJOL)

    A distinguishing feature of this Virtual Laboratory Workbench is that it allows the instructor flexibility in designing laboratory exercises so as to integrate specific knowledge objectives, outcome concepts and pre-requisites with the activity instructions. Another important benefit is that it has a watch-dog monitor that keeps a log ...

  11. DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.

    Science.gov (United States)

    Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng

    2015-10-06

    Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three 'tier' design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and 'debugging' the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems. © 2015 The Authors.

  12. Assessment of the Usability of the Workbench Faraday Cage Method

    OpenAIRE

    Sørensen, Morten; Franek, Ondrej; Christensen, Søren K.; Pedersen, Gert Frølund; Ebert, Hans

    2011-01-01

    The workbench Faraday Cage method (WBFC) is a time efficient module pre-compliance test regarding radiated emission. This work investigates the method’s usability and credibility and concludes that for this particular case the WBFC perform a tolerable compliance test for frequencies below 360 MHz while it is essentially useless for higher frequencies.

  13. Finite element simulations with ANSYS workbench 17 theory, applications, case studies

    CERN Document Server

    Lee, Huei-Huang

    2017-01-01

    Finite Element Simulations with ANSYS Workbench 17 is a comprehensive and easy to understand workbook. Printed in full color, it utilizes rich graphics and step-by-step instructions to guide you through learning how to perform finite element simulations using ANSYS Workbench. Twenty seven real world case studies are used throughout the book. Many of these case studies are industrial or research projects that you build from scratch. Prebuilt project files are available for download should you run into any problems. Companion videos, that demonstrate exactly how to perform each tutorial, are also available. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences spreads though this entire boo...

  14. Finite element simulations with ANSYS Workbench 18 theory, applications, case studies

    CERN Document Server

    Lee,\tHuei-huang

    2018-01-01

    Finite Element Simulations with ANSYS Workbench 18 is a comprehensive and easy to understand workbook. Printed in full color, it utilizes rich graphics and step-by-step instructions to guide you through learning how to perform finite element simulations using ANSYS Workbench. Twenty seven real world case studies are used throughout the book. Many of these case studies are industrial or research projects that you build from scratch. Prebuilt project files are available for download should you run into any problems. Companion videos, that demonstrate exactly how to perform each tutorial, are also available. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences is utilized though this entire...

  15. The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

    Science.gov (United States)

    Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

    2017-01-01

    RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

  16. HCI^2 Workbench: A Development Tool for Multimodal Human-Computer Interaction Systems

    NARCIS (Netherlands)

    Shen, Jie; Wenzhe, Shi; Pantic, Maja

    In this paper, we present a novel software tool designed and implemented to simplify the development process of Multimodal Human-Computer Interaction (MHCI) systems. This tool, which is called the HCI^2 Workbench, exploits a Publish / Subscribe (P/S) architecture [13] [14] to facilitate efficient

  17. A hyperspectral image data exploration workbench for environmental science applications

    International Nuclear Information System (INIS)

    Woyna, M.A.; Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.

    1994-01-01

    The Hyperspectral Image Data Exploration Workbench (HIDEW) software system has been developed by Argonne National Laboratory to enable analysts at Unix workstations to conveniently access and manipulate high-resolution imagery data for analysis, mapping purposes, and input to environmental modeling applications. HIDEW is fully object-oriented, including the underlying database. This system was developed as an aid to site characterization work and atmospheric research projects

  18. A hyperspectral image data exploration workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Woyna, M.A.; Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.

    1994-08-01

    The Hyperspectral Image Data Exploration Workbench (HIDEW) software system has been developed by Argonne National Laboratory to enable analysts at Unix workstations to conveniently access and manipulate high-resolution imagery data for analysis, mapping purposes, and input to environmental modeling applications. HIDEW is fully object-oriented, including the underlying database. This system was developed as an aid to site characterization work and atmospheric research projects.

  19. Grayscale Optical Correlator Workbench

    Science.gov (United States)

    Hanan, Jay; Zhou, Hanying; Chao, Tien-Hsin

    2006-01-01

    Grayscale Optical Correlator Workbench (GOCWB) is a computer program for use in automatic target recognition (ATR). GOCWB performs ATR with an accurate simulation of a hardware grayscale optical correlator (GOC). This simulation is performed to test filters that are created in GOCWB. Thus, GOCWB can be used as a stand-alone ATR software tool or in combination with GOC hardware for building (target training), testing, and optimization of filters. The software is divided into three main parts, denoted filter, testing, and training. The training part is used for assembling training images as input to a filter. The filter part is used for combining training images into a filter and optimizing that filter. The testing part is used for testing new filters and for general simulation of GOC output. The current version of GOCWB relies on the mathematical software tools from MATLAB binaries for performing matrix operations and fast Fourier transforms. Optimization of filters is based on an algorithm, known as OT-MACH, in which variables specified by the user are parameterized and the best filter is selected on the basis of an average result for correct identification of targets in multiple test images.

  20. Collaborative WorkBench for Researchers - Work Smarter, Not Harder

    Science.gov (United States)

    Ramachandran, Rahul; Kuo, Kwo-sen; Maskey, Manil; Lynnes, Christopher

    2014-01-01

    It is important to define some commonly used terminology related to collaboration to facilitate clarity in later discussions. We define provisioning as infrastructure capabilities such as computation, storage, data, and tools provided by some agency or similarly trusted institution. Sharing is defined as the process of exchanging data, programs, and knowledge among individuals (often strangers) and groups. Collaboration is a specialized case of sharing. In collaboration, sharing with others (usually known colleagues) is done in pursuit of a common scientific goal or objective. Collaboration entails more dynamic and frequent interactions and can occur at different speeds. Synchronous collaboration occurs in real time such as editing a shared document on the fly, chatting, video conference, etc., and typically requires a peer-to-peer connection. Asynchronous collaboration is episodic in nature based on a push-pull model. Examples of asynchronous collaboration include email exchanges, blogging, repositories, etc. The purpose of a workbench is to provide a customizable framework for different applications. Since the workbench will be common to all the customized tools, it promotes building modular functionality that can be used and reused by multiple tools. The objective of our Collaborative Workbench (CWB) is thus to create such an open and extensible framework for the Earth Science community via a set of plug-ins. Our CWB is based on the Eclipse [2] Integrated Development Environment (IDE), which is designed as a small kernel containing a plug-in loader for hundreds of plug-ins. The kernel itself is an implementation of a known specification to provide an environment for the plug-ins to execute. This design enables modularity, where discrete chunks of functionality can be reused to build new applications. The minimal set of plug-ins necessary to create a client application is called the Eclipse Rich Client Platform (RCP) [3]; The Eclipse RCP also supports thousands

  1. Building a Taxonomic Data Editor: ITIS Taxonomic Workbench 6.0

    OpenAIRE

    Mitchell,David; Bowman,Lisa; Brockmeier,Christopher

    2017-01-01

    The Integrated Taxonomic Information System (ITIS - www.itis.gov) provides a regularly updated global database that currently contains over 840,000 scientific names and their hierarchy. A new rich Internet application for adding and editing ITIS data, Taxonomic Workbench 6.0, is being developed using the AngularJS framework. AngularJS is designed to take advantage of many features that are fairly recent to the web platform, facilitates a well-structured product that is easier to maintain, and...

  2. Using registries to integrate bioinformatics tools and services into workbench environments

    DEFF Research Database (Denmark)

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer

    2016-01-01

    The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially......, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry....

  3. Validation of the thermal code of RadTherm-IR, IR-Workbench, and F-TOM

    Science.gov (United States)

    Schwenger, Frédéric; Grossmann, Peter; Malaplate, Alain

    2009-05-01

    System assessment by image simulation requires synthetic scenarios that can be viewed by the device to be simulated. In addition to physical modeling of the camera, a reliable modeling of scene elements is necessary. Software products for modeling of target data in the IR should be capable of (i) predicting surface temperatures of scene elements over a long period of time and (ii) computing sensor views of the scenario. For such applications, FGAN-FOM acquired the software products RadTherm-IR (ThermoAnalytics Inc., Calumet, USA; IR-Workbench (OKTAL-SE, Toulouse, France). Inspection of the accuracy of simulation results by validation is necessary before using these products for applications. In the first step of validation, the performance of both "thermal solvers" was determined through comparison of the computed diurnal surface temperatures of a simple object with the corresponding values from measurements. CUBI is a rather simple geometric object with well known material parameters which makes it suitable for testing and validating object models in IR. It was used in this study as a test body. Comparison of calculated and measured surface temperature values will be presented, together with the results from the FGAN-FOM thermal object code F-TOM. In the second validation step, radiances of the simulated sensor views computed by RadTherm-IR and IR-Workbench will be compared with radiances retrieved from the recorded sensor images taken by the sensor that was simulated. Strengths and weaknesses of the models RadTherm-IR, IR-Workbench and F-TOM will be discussed.

  4. Open source molecular modeling.

    Science.gov (United States)

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  5. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

    Science.gov (United States)

    Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

    2016-01-04

    The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Integrating Online and Active Learning in a Computer-Assisted Translation Workbench

    DEFF Research Database (Denmark)

    Alabau, Vicent; González-Rubio, Jésus; Ortíz-Martínez, Daniel

    2014-01-01

    This paper describes a pilot study with a computed-assisted translation workbench aiming at testing the integration of online and active learning features. We investigate the effect of these features on translation productivity, using interactive translation prediction (ITP) as a baseline. User...... activity data were collected from five beta testers using key-logging and eye-tracking. User feedback was also collected at the end of the experiments in the form of retrospective think-aloud protocols. We found that OL performs better than ITP, especially in terms of translation speed. In addition, AL...

  7. Finite element simulations with ANSYS workbench 16

    CERN Document Server

    Lee , Huei-Huang

    2015-01-01

    Finite Element Simulations with ANSYS Workbench 16 is a comprehensive and easy to understand workbook. It utilizes step-by-step instructions to help guide readers to learn finite element simulations. Twenty seven real world case studies are used throughout the book. Many of these cases are industrial or research projects the reader builds from scratch. All the files readers may need if they have trouble are available for download on the publishers website. Companion videos that demonstrate exactly how to preform each tutorial are available to readers by redeeming the access code that comes in the book. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences spreads through this entire book. A...

  8. CH2 molecular beam source

    International Nuclear Information System (INIS)

    Porter, R.A.R.; Grosser, A.E.

    1980-01-01

    A molecular beam source of CH 2 is described. Coaxial beams of methylene halide and alkali metal react and the mixture is formed into a molecular beam. Passage through a mechanical velocity selector rotating at a suitably high speed purifies the beam, separating light, fast CH 2 from heavier, slower contaminating species

  9. A workbench for tera-flop supercomputing

    International Nuclear Information System (INIS)

    Resch, M.M.; Kuester, U.; Mueller, M.S.; Lang, U.

    2003-01-01

    Supercomputers currently reach a peak performance in the range of TFlop/s. With but one exception - the Japanese Earth Simulator - none of these systems has so far been able to also show a level of sustained performance for a variety of applications that comes close to the peak performance. Sustained TFlop/s are therefore rarely seen. The reasons are manifold and are well known: Bandwidth and latency both for main memory and for the internal network are the key internal technical problems. Cache hierarchies with large caches can bring relief but are no remedy to the problem. However, there are not only technical problems that inhibit the full exploitation by scientists of the potential of modern supercomputers. More and more organizational issues come to the forefront. This paper shows the approach of the High Performance Computing Center Stuttgart (HLRS) to deliver a sustained performance of TFlop/s for a wide range of applications from a large group of users spread over Germany. The core of the concept is the role of the data. Around this we design a simulation workbench that hides the complexity of interacting computers, networks and file systems from the user. (authors)

  10. A hyperspectral image analysis workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.; Slater, J.C.

    1992-10-01

    A significant challenge to the information sciences is to provide more powerful and accessible means to exploit the enormous wealth of data available from high-resolution imaging spectrometry, or ``hyperspectral`` imagery, for analysis, for mapping purposes, and for input to environmental modeling applications. As an initial response to this challenge, Argonne`s Advanced Computer Applications Center has developed a workstation-based prototype software workbench which employs Al techniques and other advanced approaches to deduce surface characteristics and extract features from the hyperspectral images. Among its current capabilities, the prototype system can classify pixels by abstract surface type. The classification process employs neural network analysis of inputs which include pixel spectra and a variety of processed image metrics, including image ``texture spectra`` derived from fractal signatures computed for subimage tiles at each wavelength.

  11. abc the aspectBench compiler for aspectJ a workbench for aspect-oriented programming language and compilers research

    DEFF Research Database (Denmark)

    Allan, Chris; Avgustinov, Pavel; Christensen, Aske Simon

    2005-01-01

    Aspect-oriented programming (AOP) is gaining popularity as a new way of modularising cross-cutting concerns. The aspectbench compiler (abc) is a new workbench for AOP research which provides an extensible research framework for both new language features and new compiler optimisations. This poste...

  12. WORKBENCH FOR CONTROL SYSTEMS TRIALS BASED ON VIPA 300 CONTROLLER AND ADVANTECH INPUT/OUTPUT CARD

    Directory of Open Access Journals (Sweden)

    M. V. Levinskyi

    2015-01-01

    Full Text Available The topic is about workbench creation for control systems trials based on VIPA 300 industrial PLC and model of control object which is implemented in MatLab Simulink program on PC. Connection between controller and the PC is provided by the Advantech PCI-1711 input/output card of discrete and analog signals. Object identification,control system synthesis, creation of control device structure and its parametrical identification, as a rule, is done on a PC in a modelling environment, e.g. in MatLab. But often, using this PC modelling, the hardware and software features of algorithms which were obtained during system synthesis are not considered in a specific industrial PLC.It is considered a good idea to use a composite version where obtained algorithms are tested in a real industrial PLC and control object is substituted by a model which is working on a PC in real time scale. In this case software realization of algorithms in a specific PLC are fully taken into account and substitution of real control object by itsmodel considerably reduces the costs for carrying out experiments and allows to study the system behavior when control object parameters and modes of operation vary greatly. The creation of workbench stipulates several stages: configuration and programming of industrial PLC VIPA 313 SC, installation and configuration of Advantech PCI- 1711 input/output card, tuning of Simulink modelling environment for working in real time scale using Real-Time Windows Target Library, testing of workbench by using constant and harmonic signals of different frequencies. Work results of virtual stabilization system are compared with combined version. In virtual stabilization system PID governor and control object are implemented in Simulink. In combined version control object is still implemented in Simulink and PID governor - in VIPA 313 SC controller (using functional block FB58 from Step7 standard library.

  13. A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

    Science.gov (United States)

    Smelter, Andrey; Moseley, Hunter N B

    2018-01-01

    variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

  14. A Versatile Internet-Accessible Electronics Workbench with Troubleshooting Capabilities

    Directory of Open Access Journals (Sweden)

    Hamidou Soumare

    2009-08-01

    Full Text Available The MIT iLab Project was established to expand the range of laboratory experiences available to students in science and engineering education. iLabs are online laboratories that enable students to conduct real experiments remotely. Recently, the iLab Project has focused on building remote laboratories around the NI-ELVIS platform, an all-in-one electronics workbench. This paper will detail our recent efforts in expanding the capabilities of ELVIS-based iLabs by enabling students to test and debug digital and analog circuits. This work will enable students to perform remote experiments characterizing digital logic elements. By merging switching capabilities with the Digital Multimeter available on the ELVIS, students will have the ability to examine and troubleshoot circuits. These added capabilities will provide educators and students with unparalleled flexibility and significantly enrich the remote laboratory experience.

  15. A hyperspectral image analysis workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.; Slater, J.C.

    1992-01-01

    A significant challenge to the information sciences is to provide more powerful and accessible means to exploit the enormous wealth of data available from high-resolution imaging spectrometry, or hyperspectral'' imagery, for analysis, for mapping purposes, and for input to environmental modeling applications. As an initial response to this challenge, Argonne's Advanced Computer Applications Center has developed a workstation-based prototype software workbench which employs Al techniques and other advanced approaches to deduce surface characteristics and extract features from the hyperspectral images. Among its current capabilities, the prototype system can classify pixels by abstract surface type. The classification process employs neural network analysis of inputs which include pixel spectra and a variety of processed image metrics, including image texture spectra'' derived from fractal signatures computed for subimage tiles at each wavelength.

  16. M3MS-16OR0401086 – Report on NEAMS Workbench Support for MOOSE Applications

    Energy Technology Data Exchange (ETDEWEB)

    Lefebvre, Robert A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division; Langley, Brandon R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division; Thompson, Adam B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division

    2016-09-23

    This report summarizes the status of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench from Oak Ridge National Laboratory (ORNL) and the integration of the MOOSE framework. This report marks the completion of NEAMS milestone M3MS-16OR0401086. This report documents the developed infrastructure to support the MOOSE framework applications, the applications’ results, visualization status, the collaboration that facilitated this progress, and future considerations.

  17. HDX Workbench: Software for the Analysis of H/D Exchange MS Data

    Science.gov (United States)

    Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

    2012-09-01

    Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

  18. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

    Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

  19. TCW: transcriptome computational workbench.

    Science.gov (United States)

    Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

    2013-01-01

    The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

  20. The chemistry of molecular anions in circumstellar sources

    Energy Technology Data Exchange (ETDEWEB)

    Agúndez, Marcelino [LUTH, Observatoire de Paris-Meudon, 5 Place Jules Janssen, 92190 Meudon (France); Cernicharo, José [Departamento de Astrofísica, CAB, CSIC-INTA, Ctra. de Torrejón a Ajalvir km 4, 28850 Madrid (Spain); Guélin, Michel [Institut de Radioastronomie Millimétrique, 300 rue de la Piscine, 38406 Saint Martin d' Héres (France)

    2015-01-22

    The detection of negatively charged molecules in the interstellar and circumstellar medium in the past four years has been one of the most impacting surprises in the area of molecular astrophysics. It has motivated the interest of astronomers, physicists, and chemists on the study of the spectroscopy, chemical kinetics, and prevalence of molecular anions in the different astronomical regions. Up to six different molecular anions have been discovered in space to date, the last one being the small ion CN{sup −}, which has been observed in the envelope of the carbon star IRC +10216 and which contrary to the other larger anions is not formed by electron attachment to CN, but through reactions of large carbon anions with nitrogen atoms. Here we briefly review the current status of our knowledge of the chemistry of molecular anions in space, with particular emphasis on the circumstellar source IRC +10216, which to date is the astronomical source harboring the largest variety of anions.

  1. Molecular environmental science and synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G.E. Jr. [Stanford Univ., CA (United States)

    1995-12-31

    Molecular environmental science is a relatively new field but focuses on the chemical and physical forms of toxic and/or radioactive contaminants in soils, sediments, man-made waste forms, natural waters, and the atmosphere; their possible reactions with inorganic and organic compounds, plants, and organisms in the environment; and the molecular-level factors that control their toxicity, bioavailability, and transport. The chemical speciation of a contaminant is a major factor in determining its behavior in the environment, and synchrotron-based X-ray absorption fine structure (XAFS) spectroscopy is one of the spectroscopies of choice to quantitatively determine speciation of heavy metal contaminants in situ without selective extraction or other sample treatment. The use of high-flux insertion device beam lines at synchrotron sources and multi-element array detectors has permitted XAFS studies of metals such as Se and As in natural soils at concentration levels as low as 50 ppm. The X-ray absorption near edge structure of these metals is particularly useful in determining their oxidation state. Examples of such studies will be presented, and new insertion device beam lines under development at SSRL and the Advanced Photon Source for molecular environmental science applications will be discussed.

  2. Language workbench user interfaces for data analysis

    Directory of Open Access Journals (Sweden)

    Victoria M. Benson

    2015-02-01

    Full Text Available Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/.

  3. Language workbench user interfaces for data analysis

    Science.gov (United States)

    Benson, Victoria M.

    2015-01-01

    Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/). PMID:25755929

  4. Neural networks used to monitor an experimental test workbench

    Energy Technology Data Exchange (ETDEWEB)

    Moraes, Davi Almeida; Pereira, Iraci Martinez, E-mail: dmoraes@dk8.com.br, E-mail: martinez@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-07-01

    This work presents the application of neural networks in an experimental workbench. This bench was developed with the purpose of conducting real time tests and data acquisition. The method applied for this work allowed to generate faulty data in a gradual and controlled way through the binary combination of double action valves. Using the SCADA application (Supervisory Control and Data Acquisition), it became possible to acquire data for analysis in Matlab / Simulink software. This bench has two reservoirs: a reservoir that has sensors for recording pressure and temperature variables for later analysis, and another reservoir that has level sensors. Four models were used to develop the respective practical experiments. In the first model, it was possible to perform all practical tests of the plant, as well as mechanical changes like repositioning of some mechanical components, piping, sensors and electrovalves. In the second model, it was noticed that the positioning of the flow meter, located after the pump output, prevented a good measurement of the flow variable. In the third model, it was perceived that the number of failures initially adopted, made the data too confusing for the neural network analysis. In the last model, it was possible to obtain a performance of 96.6% of hits after the reconfiguration for 4 controlled faults. (author)

  5. Neural networks used to monitor an experimental test workbench

    International Nuclear Information System (INIS)

    Moraes, Davi Almeida; Pereira, Iraci Martinez

    2017-01-01

    This work presents the application of neural networks in an experimental workbench. This bench was developed with the purpose of conducting real time tests and data acquisition. The method applied for this work allowed to generate faulty data in a gradual and controlled way through the binary combination of double action valves. Using the SCADA application (Supervisory Control and Data Acquisition), it became possible to acquire data for analysis in Matlab / Simulink software. This bench has two reservoirs: a reservoir that has sensors for recording pressure and temperature variables for later analysis, and another reservoir that has level sensors. Four models were used to develop the respective practical experiments. In the first model, it was possible to perform all practical tests of the plant, as well as mechanical changes like repositioning of some mechanical components, piping, sensors and electrovalves. In the second model, it was noticed that the positioning of the flow meter, located after the pump output, prevented a good measurement of the flow variable. In the third model, it was perceived that the number of failures initially adopted, made the data too confusing for the neural network analysis. In the last model, it was possible to obtain a performance of 96.6% of hits after the reconfiguration for 4 controlled faults. (author)

  6. Carbon nanotube forests: a non-stick workbench for nanomanipulation

    International Nuclear Information System (INIS)

    Gjerde, Kjetil; Kjelstrup-Hansen, Jakob; Clausen, Casper H; Teo, Kenneth B K; Milne, William I; Rubahn, Horst-Guenter; Boeggild, Peter

    2006-01-01

    The ubiquitous static friction (stiction) and adhesion forces comprise a major obstacle in the manipulation of matter at the nanoscale (Falvo et al 1999 Nature 397 236; Urbakh M et al 2004 Nature 430 525). In this work it is shown that a surface coated with vertically aligned carbon nanotubes-a nanotube forest-acts as an effective non-stick workbench for the manipulation of micro-objects and fibres/wires with one or more dimensions in the nano-range. These include organic nanofibres (Balzer and Rubahn 2001 Appl. Phys. Lett. 79 3860) and microsized latex beads, which adhere strongly even to a conventional low surface-energy material like Teflon. Although organic nanofibres are attractive as device components due to their chemical adaptability, adhesion forces nearly always rule out manipulation as a route to assembly of prototype devices based on such materials, because organic materials are soft and fragile, and tend to stick to any surface. We demonstrate here that the nanotube forest due to its roughness not only exhibits very low stiction and dynamic friction; it also acts as a springy and mechanically compliant surface, making it possible to lift up and manipulate delicate nanostructures such as organic nanofibres in ways not possible on planar, rigid surfaces

  7. Automated Source Code Analysis to Identify and Remove Software Security Vulnerabilities: Case Studies on Java Programs

    OpenAIRE

    Natarajan Meghanathan

    2013-01-01

    The high-level contribution of this paper is to illustrate the development of generic solution strategies to remove software security vulnerabilities that could be identified using automated tools for source code analysis on software programs (developed in Java). We use the Source Code Analyzer and Audit Workbench automated tools, developed by HP Fortify Inc., for our testing purposes. We present case studies involving a file writer program embedded with features for password validation, and ...

  8. Multisample matrix-assisted laser desorption source for molecular beams of neutral peptides

    International Nuclear Information System (INIS)

    Lupulescu, C.; Abd El Rahim, M.; Antoine, R.; Barbaire, M.; Broyer, M.; Dagany, X.; Maurelli, J.; Rayane, D.; Dugourd, Ph.

    2006-01-01

    We developed and tested a multisample laser desorption source for producing stable molecular beams of neutral peptides. Our apparatus is based on matrix-assisted laser desorption technique. The source consists of 96 different targets which may be scanned by a software control procedure. Examples of molecular beams of neutral peptides are presented, as well as the influence of the different source parameters on the jet

  9. New impressive capabilities of SE-workbench for EO/IR real-time rendering of animated scenarios including flares

    Science.gov (United States)

    Le Goff, Alain; Cathala, Thierry; Latger, Jean

    2015-10-01

    To provide technical assessments of EO/IR flares and self-protection systems for aircraft, DGA Information superiority resorts to synthetic image generation to model the operational battlefield of an aircraft, as viewed by EO/IR threats. For this purpose, it completed the SE-Workbench suite from OKTAL-SE with functionalities to predict a realistic aircraft IR signature and is yet integrating the real-time EO/IR rendering engine of SE-Workbench called SE-FAST-IR. This engine is a set of physics-based software and libraries that allows preparing and visualizing a 3D scene for the EO/IR domain. It takes advantage of recent advances in GPU computing techniques. The recent past evolutions that have been performed concern mainly the realistic and physical rendering of reflections, the rendering of both radiative and thermal shadows, the use of procedural techniques for the managing and the rendering of very large terrains, the implementation of Image- Based Rendering for dynamic interpolation of plume static signatures and lastly for aircraft the dynamic interpolation of thermal states. The next step is the representation of the spectral, directional, spatial and temporal signature of flares by Lacroix Defense using OKTAL-SE technology. This representation is prepared from experimental data acquired during windblast tests and high speed track tests. It is based on particle system mechanisms to model the different components of a flare. The validation of a flare model will comprise a simulation of real trials and a comparison of simulation outputs to experimental results concerning the flare signature and above all the behavior of the stimulated threat.

  10. The coupling of MATISSE and the SE-WORKBENCH: a new solution for simulating efficiently the atmospheric radiative transfer and the sea surface radiation

    Science.gov (United States)

    Cathala, Thierry; Douchin, Nicolas; Latger, Jean; Caillault, Karine; Fauqueux, Sandrine; Huet, Thierry; Lubarre, Luc; Malherbe, Claire; Rosier, Bernard; Simoneau, Pierre

    2009-05-01

    The SE-WORKBENCH workshop, also called CHORALE (French acceptation for "simulated Optronic Acoustic Radar battlefield") is used by the French DGA (MoD) and several other Defense organizations and companies all around the World to perform multi-sensors simulations. CHORALE enables the user to create virtual and realistic multi spectral 3D scenes that may contain several types of target, and then generate the physical signal received by a sensor, typically an IR sensor. The SE-WORKBENCH can be used either as a collection of software modules through dedicated GUIs or as an API made of a large number of specialized toolkits. The SE-WORKBENCH is made of several functional block: one for geometrically and physically modeling the terrain and the targets, one for building the simulation scenario and one for rendering the synthetic environment, both in real and non real time. Among the modules that the modeling block is composed of, SE-ATMOSPHERE is used to simulate the atmospheric conditions of a Synthetic Environment and then to integrate the impact of these conditions on a scene. This software product generates an exploitable physical atmosphere by the SE WORKBENCH tools generating spectral images. It relies on several external radiative transfer models such as MODTRAN V4.2 in the current version. MATISSE [4,5] is a background scene generator developed for the computation of natural background spectral radiance images and useful atmospheric radiative quantities (radiance and transmission along a line of sight, local illumination, solar irradiance ...). Backgrounds include atmosphere, low and high altitude clouds, sea and land. A particular characteristic of the code is its ability to take into account atmospheric spatial variability (temperatures, mixing ratio, etc) along each line of sight. An Application Programming Interface (API) is included to facilitate its use in conjunction with external codes. MATISSE is currently considered as a new external radiative transfer

  11. Pumping requirements and options for molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

    International Nuclear Information System (INIS)

    McCollum, M.J.; Plano, M.A.; Haase, M.A.; Robbins, V.M.; Jackson, S.L.; Cheng, K.Y.; Stillman, G.E.

    1989-01-01

    This paper discusses the use of gas sources in growth by MBE as a result of current interest in growth of InP/InGaAsP/InGaAs lattice matched to InP. For gas flows greater than a few sccm, pumping speed requirements dictate the use of turbomolecular or diffusion pumps. GaAs samples with high p-type mobilities have been grown with diffusion pumped molecular beam epitaxial system. According to the authors, this demonstration of the inherent cleanliness of a properly designed diffusion pumping system indicates that a diffusion pump is an excellent inexpensive and reliable choice for growth by molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

  12. Moving Towards a Science-Driven Workbench for Earth Science Solutions

    Science.gov (United States)

    Graves, S. J.; Djorgovski, S. G.; Law, E.; Yang, C. P.; Keiser, K.

    2017-12-01

    The NSF-funded EarthCube Integration and Test Environment (ECITE) prototype was proposed as a 2015 Integrated Activities project and resulted in the prototyping of an EarthCube federated cloud environment and the Integration and Testing Framework. The ECITE team has worked with EarthCube science and technology governance committees to define the types of integration, testing and evaluation necessary to achieve and demonstrate interoperability and functionality that benefit and support the objectives of the EarthCube cyber-infrastructure. The scope of ECITE also includes reaching beyond NSF and EarthCube to work with the broader Earth science community, such as the Earth Science Information Partners (ESIP) to incorporate lessons learned from other testbed activities, and ultimately provide broader community benefits. This presentation will discuss evolving ECITE ideas for a science-driven workbench that will start with documented science use cases, map the use cases to solution scenarios that identify the available technology and data resources that match the use case, the generation of solution workflows and test plans, the testing and evaluation of the solutions in a cloud environment, and finally the documentation of identified technology and data gaps that will assist with driving the development of additional EarthCube resources.

  13. Evaluation of climatic vibration testing on plastic waterproof enclosure for electronic equipment using ANSYS[reg] workbench

    International Nuclear Information System (INIS)

    Aw, K.C.; Huang, W.D.J.; De Silva, M.W.R.P.

    2007-01-01

    Designing and testing of waterproof enclosure for electronic equipment involves significant amount of time and resources. This paper concentrates on electronic equipment used for maritime application. Typical waterproof test perform is based on the IEC 60529 standards and is insufficient to determine its reliability. Since, these enclosures were subjected to environmental stress such as heat and vibration and there is a need to understand how these affect the waterproof performance. Simulation using ANSYS workbench software was performed to comprehend the effect of various parameters of accelerated testing performed on these waterproof enclosures. Experiments were performed to examine the correlation with simulation results. The results confirmed that accelerated testing with random vibration at cold temperature causes greatest stress and causes degradation to adhesive bonds and hence affect the waterproof performance

  14. Molecular and negative ion production by a standard electron cyclotron resonance ion source

    Energy Technology Data Exchange (ETDEWEB)

    Racz, R. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary); Biri, S.; Juhasz, Z.; Sulik, B. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); Palinkas, J. [University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary)

    2012-02-15

    Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H{sup -}, O{sup -}, OH{sup -}, O{sub 2}{sup -}, C{sup -}, C{sub 60}{sup -} negative ions and H{sub 2}{sup +}, H{sub 3}{sup +}, OH{sup +}, H{sub 2}O{sup +}, H{sub 3}O{sup +}, O{sub 2}{sup +} positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several {mu}A and positive molecular ion beams in the mA range were successfully obtained.

  15. Pteros: fast and easy to use open-source C++ library for molecular analysis.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2012-07-15

    An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

  16. An agile acquisition decision-support workbench for evaluating ISR effectiveness

    Science.gov (United States)

    Stouch, Daniel W.; Champagne, Valerie; Mow, Christopher; Rosenberg, Brad; Serrin, Joshua

    2011-06-01

    The U.S. Air Force is consistently evolving to support current and future operations through the planning and execution of intelligence, surveillance and reconnaissance (ISR) missions. However, it is a challenge to maintain a precise awareness of current and emerging ISR capabilities to properly prepare for future conflicts. We present a decisionsupport tool for acquisition managers to empirically compare ISR capabilities and approaches to employing them, thereby enabling the DoD to acquire ISR platforms and sensors that provide the greatest return on investment. We have developed an analysis environment to perform modeling and simulation-based experiments to objectively compare alternatives. First, the analyst specifies an operational scenario for an area of operations by providing terrain and threat information; a set of nominated collections; sensor and platform capabilities; and processing, exploitation, and dissemination (PED) capacities. Next, the analyst selects and configures ISR collection strategies to generate collection plans. The analyst then defines customizable measures of effectiveness or performance to compute during the experiment. Finally, the analyst empirically compares the efficacy of each solution and generates concise reports to document their conclusions, providing traceable evidence for acquisition decisions. Our capability demonstrates the utility of using a workbench environment for analysts to design and run experiments. Crafting impartial metrics enables the acquisition manager to focus on evaluating solutions based on specific military needs. Finally, the metric and collection plan visualizations provide an intuitive understanding of the suitability of particular solutions. This facilitates a more agile acquisition strategy that handles rapidly changing technology in response to current military needs.

  17. FiGS: a filter-based gene selection workbench for microarray data

    Directory of Open Access Journals (Sweden)

    Yun Taegyun

    2010-01-01

    Full Text Available Abstract Background The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset. Results FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs. Conclusion FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.

  18. The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster

    Science.gov (United States)

    Löwe, P.; Klump, J.; Thaler, J.

    2012-04-01

    Compute clusters can be used as GIS workbenches, their wealth of resources allow us to take on geocomputation tasks which exceed the limitations of smaller systems. To harness these capabilities requires a Geographic Information System (GIS), able to utilize the available cluster configuration/architecture and a sufficient degree of user friendliness to allow for wide application. In this paper we report on the first successful porting of GRASS GIS, the oldest and largest Free Open Source (FOSS) GIS project, onto a compute cluster using Platform Computing's Load Sharing Facility (LSF). In 2008, GRASS6.3 was installed on the GFZ compute cluster, which at that time comprised 32 nodes. The interaction with the GIS was limited to the command line interface, which required further development to encapsulate the GRASS GIS business layer to facilitate its use by users not familiar with GRASS GIS. During the summer of 2011, multiple versions of GRASS GIS (v 6.4, 6.5 and 7.0) were installed on the upgraded GFZ compute cluster, now consisting of 234 nodes with 480 CPUs providing 3084 cores. The GFZ compute cluster currently offers 19 different processing queues with varying hardware capabilities and priorities, allowing for fine-grained scheduling and load balancing. After successful testing of core GIS functionalities, including the graphical user interface, mechanisms were developed to deploy scripted geocomputation tasks onto dedicated processing queues. The mechanisms are based on earlier work by NETELER et al. (2008). A first application of the new GIS functionality was the generation of maps of simulated tsunamis in the Mediterranean Sea for the Tsunami Atlas of the FP-7 TRIDEC Project (www.tridec-online.eu). For this, up to 500 processing nodes were used in parallel. Further trials included the processing of geometrically complex problems, requiring significant amounts of processing time. The GIS cluster successfully completed all these tasks, with processing times

  19. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Model-based evaluation of the use of polycyclic aromatic hydrocarbons molecular diagnostic ratios as a source identification tool

    International Nuclear Information System (INIS)

    Katsoyiannis, Athanasios; Breivik, Knut

    2014-01-01

    Polycyclic Aromatic Hydrocarbons (PAHs) molecular diagnostic ratios (MDRs) are unitless concentration ratios of pair-PAHs with the same molecular weight (MW); MDRs have long been used as a tool for PAHs source identification purposes. In the present paper, the efficiency of the MDR methodology is evaluated through the use of a multimedia fate model, the calculation of characteristic travel distances (CTD) and the estimation of air concentrations for individual PAHs as a function of distance from an initial point source. The results show that PAHs with the same MW are sometimes characterized by substantially different CTDs and therefore their air concentrations and hence MDRs are predicted to change as the distance from the original source increases. From the assessed pair-PAHs, the biggest CTD difference is seen for Fluoranthene (107 km) vs. Pyrene (26 km). This study provides a strong indication that MDRs are of limited use as a source identification tool. -- Highlights: • Model-based evaluation of the PAHs molecular diagnostic ratios efficiency. • Individual PAHs are characterized by different characteristic travel distances. • MDRs are proven to be a limited tool for source identification. • Use of MDRs for other environmental media is likely unfeasible. -- PAHs molecular diagnostic ratios which change greatly as a function of distance from the emitting source are improper for source identification purposes

  1. The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

    Energy Technology Data Exchange (ETDEWEB)

    Sunderam, Vaidy S.

    2012-03-20

    The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.

  2. Atomic and molecular spectroscopy with optical-frequency-comb-referenced IR coherent sources

    International Nuclear Information System (INIS)

    Cancio, P.; Bartalini, S.; De Rosa, M.; Giusfredi, G.; Mazzotti, D.; Maddaloni, P.; Vitiello, M. S.; De Natale, P.

    2013-01-01

    We provide a review of progress in the development of metrological-grade measurements in atomic and molecular systems through the extension, in the mid-infrared and far-infrared range, of optical frequency combs (OFCs) and the introduction of new techniques and highly coherent sources. (authors)

  3. Integrating open-source software applications to build molecular dynamics systems.

    Science.gov (United States)

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-05

    Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

  4. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, Ken R. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305 (United States); Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Coffee, Ryan [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Curiel, G. Ivan; Holmes, Michael; Krzywinski, Jacek; Messerschmidt, Marc; Minitti, Michael; Mitra, Ankush; Moeller, Stefan; Noonan, Peter; Osipov, Timur; Schorb, Sebastian; Swiggers, Michele; Wallace, Alexander; Yin, Jing [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Bostedt, Christoph, E-mail: bostedt@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-17

    A description of the Atomic, Molecular and Optical Sciences (AMO) instrument at the Linac Coherent Light Source is presented. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument. The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump–probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

  5. Source-specific sewage pollution detection in urban river waters using pharmaceuticals and personal care products as molecular indicators.

    Science.gov (United States)

    Kiguchi, Osamu; Sato, Go; Kobayashi, Takashi

    2016-11-01

    Source-specific elucidation of domestic sewage pollution caused by various effluent sources in an urban river water, as conducted for this study, demands knowledge of the relation between concentrations of pharmaceuticals and personal care products (PPCPs) as molecular indicators (caffeine, carbamazepine, triclosan) and water quality concentrations of total nitrogen (T-N) and total phosphorous (T-P). River water and wastewater samples from the Asahikawa River Basin in northern Japan were analyzed using derivatization-gas chromatography/mass spectrometry. Caffeine, used as an indicator of domestic sewage in the Asahikawa River Basin, was more ubiquitous than either carbamazepine or triclosan (92-100 %). Its concentration was higher than any target compound used to assess the basin: caffeine, caffeine concentrations detected in wastewater effluents and the strongly positive mutual linear correlation between caffeine and T-N or T-P (R 2  > 0.759) reflect the contribution of septic tank system effluents to the lower Asahikawa River Basin. Results of relative molecular indicators in combination with different molecular indicators (caffeine/carbamazepine and triclosan/carbamazepine) and cluster analysis better reflect the contribution of sewage than results obtained using concentrations of respective molecular indicators and cluster analysis. Relative molecular indicators used with water quality parameters (e.g., caffeine/T-N ratio) in this study provide results more clearly, relatively, and quantitatively than results obtained using molecular indicators alone. Moreover, the caffeine/T-N ratio reflects variations of caffeine flux from effluent sources. These results suggest strongly relative molecular indicators are also useful indicators, reflecting differences in spatial contributions of domestic sources for PPCPs in urban areas.

  6. Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2018-02-01

    Full Text Available Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX. Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.

  7. Molecular dynamics simulation of chemical vapor deposition of amorphous carbon. Dependence on H/C ratio of source gas

    International Nuclear Information System (INIS)

    Ito, Atsushi M.; Takayama, Arimichi; Nakamura, Hiroaki; Saito, Seiki; Ohno, Noriyasu; Kajita, Shin

    2011-01-01

    By molecular dynamics simulation, the chemical vapor deposition of amorphous carbon onto graphite and diamond surfaces was studied. In particular, we investigated the effect of source H/C ratio, which is the ratio of the number of hydrogen atoms to the number of carbon atoms in a source gas, on the deposition process. In the present simulation, the following two source gas conditions were tested: one was that the source gas was injected as isolated carbon and hydrogen atoms, and the other was that the source gas was injected as hydrocarbon molecules. Under the former condition, we found that as the source H/C ratio increases, the deposition rate of carbon atoms decreases exponentially. This exponential decrease in the deposition rate with increasing source H/C ratio agrees with experimental data. However, under the latter molecular source condition, the deposition rate did not decrease exponentially because of a chemical reaction peculiar to the type of hydrocarbon in the source gas. (author)

  8. Atmospheric-pressure solution-cathode glow discharge: A versatile ion source for atomic and molecular mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Andrew J. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Williams, Kelsey L. [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Hieftje, Gary M. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Shelley, Jacob T., E-mail: shellj@rpi.edu [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States)

    2017-01-15

    An atmospheric-pressure solution-cathode glow discharge (SCGD) has been evaluated as an ion source for atomic, molecular, and ambient desorption/ionization mass spectrometry. The SCGD consists of a direct-current plasma, supported in the ambient air in the absence of gas flows, and sustained upon the surface of a flowing liquid cathode. Analytes introduced in the flowing liquid, as an ambient gas, or as a solid held near the plasma are vaporized and ionized by interactions within or near the discharge. Introduction of acidic solutions containing metal salts produced bare elemental ions as well as H{sub 2}O, OH{sup −} and NO{sub 3}{sup −} adducts. Detection limits for these elemental species ranged from 0.1 to 4 ppb, working curves spanned more than 4 orders of linear dynamic range, and precision varied between 5 and 16% relative standard deviation. Small organic molecules were also efficiently ionized from solution, and both the intact molecular ion and fragments were observed in the resulting SCGD mass spectra. Fragmentation of molecular species was found to be tunable; high discharge currents led to harder ionization, while low discharge currents produced stronger molecular-ion signals. Ambient gases and solids, desorbed by the plasma from a glass probe, were also readily ionized by the SCGD. Indeed, strong analyte signals were obtained from solid samples placed at least 2 cm from the plasma. These findings indicate that the SCGD might be useful also for ambient desorption/ionization mass spectrometry. Combined with earlier results that showed the SCGD is useful for ionization of labile biomolecules, the results here indicate that the SCGD is a highly versatile ion source capable of providing both elemental and molecular mass-spectral information. - Highlights: • Solution-cathode glow discharge used as an ionization source for mass spectrometry. • SCGD-MS can provide atomic as well as intact molecular mass spectra. • Atomic limits of detection range

  9. Detailed Source-Specific Molecular Composition of Ambient Aerosol Organic Matter Using Ultrahigh Resolution Mass Spectrometry and 1H NMR

    Directory of Open Access Journals (Sweden)

    Amanda S. Willoughby

    2016-06-01

    Full Text Available Organic aerosols (OA are universally regarded as an important component of the atmosphere that have far-ranging impacts on climate forcing and human health. Many of these impacts are related to OA molecular characteristics. Despite the acknowledged importance, current uncertainties related to the source apportionment of molecular properties and environmental impacts make it difficult to confidently predict the net impacts of OA. Here we evaluate the specific molecular compounds as well as bulk structural properties of total suspended particulates in ambient OA collected from key emission sources (marine, biomass burning, and urban using ultrahigh resolution mass spectrometry (UHR-MS and proton nuclear magnetic resonance spectroscopy (1H NMR. UHR-MS and 1H NMR show that OA within each source is structurally diverse, and the molecular characteristics are described in detail. Principal component analysis (PCA revealed that (1 aromatic nitrogen species are distinguishing components for these biomass burning aerosols; (2 these urban aerosols are distinguished by having formulas with high O/C ratios and lesser aromatic and condensed aromatic formulas; and (3 these marine aerosols are distinguished by lipid-like compounds of likely marine biological origin. This study provides a unique qualitative approach for enhancing the chemical characterization of OA necessary for molecular source apportionment.

  10. Near-infrared sources in the molecular cloud G35.2-0.74

    International Nuclear Information System (INIS)

    Tapia, M.; Roth, M.; Persi, P.; Ferrari-Toniolo, M.

    1985-01-01

    Near-infrared (1-4 μm) observations of the molecular cloud G35.2-0.74 reveal the presence of four infrared sources in the vicinity of two previously reported centres of recent star formation. The northern part of G35.2-0.74 contains three point sources which are interpreted as highly obscured stars. Irs 1 coincides with H 2 O and OH maser sources and seems to be a very young early-type star. The southern part of G35.2-0.74 shows a diffuse 2.2-μm source with a flux distribution in the short-wavelength region compatible with free-free emission and a large excess at lambda > or approx. 3 μm attributed to warm dust mixed with the gas. These data are consistent with a fully developed HII region. (author)

  11. mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

    Science.gov (United States)

    Dalke, Andrew; Hert, Jérôme; Kramer, Christian

    2018-05-29

    Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

  12. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  13. Identification of the sources of primary organic aerosols at urban schools: A molecular marker approach

    International Nuclear Information System (INIS)

    Crilley, Leigh R.; Qadir, Raeed M.; Ayoko, Godwin A.; Schnelle-Kreis, Jürgen; Abbaszade, Gülcin; Orasche, Jürgen; Zimmermann, Ralf; Morawska, Lidia

    2014-01-01

    Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children's exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools. - Highlights: • Selected organic molecular markers at 11 urban schools were analyzed. • Four sources of primary organic aerosols were identified by PMF at the schools. • Both local and regional sources were found to influence exposure at the schools. • The results have implications for mitigation of children's exposure at schools. - The identification of the most important sources of primary organic aerosols at urban schools has implications for control strategies for mitigating children's exposure at schools

  14. A new approach to the method of source-sink potentials for molecular conduction

    Energy Technology Data Exchange (ETDEWEB)

    Pickup, Barry T., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Fowler, Patrick W., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Borg, Martha [Department of Chemistry, University of Sheffield, Sheffield S3 7HF (United Kingdom); Sciriha, Irene [Department of Mathematics, University of Malta, Msida (Malta)

    2015-11-21

    We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue of the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.

  15. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    Science.gov (United States)

    González-Candelas, Fernando; Bracho, María Alma; Wróbel, Borys; Moya, Andrés

    2013-07-19

    Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus. We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak. We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

  16. Molecular marker analysis as a guide to the sources of fine organic aerosols

    International Nuclear Information System (INIS)

    Rogge, W.F.; Cass, G.R.; Hildemann, L.M.; Simoneit, B.R.T.

    1992-07-01

    The molecular composition of fine particulate (D p ≥ 2 μm) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available

  17. The Advanced Light Source: A new tool for research in atomic and molecular physics

    International Nuclear Information System (INIS)

    Schlachter, F.; Robinson, A.

    1991-04-01

    The Advanced Light Source at the Lawrence Berkeley Laboratory will be the world's brightest synchrotron radiation source in the extreme ultraviolet and soft x-ray regions of the spectrum when it begins operation in 1993. It will be available as a national user facility to researchers in a broad range of disciplines, including materials science, atomic and molecular physics, chemistry, biology, imaging, and technology. The high brightness of the ALS will be particularly well suited to high-resolution studies of tenuous targets, such as excited atoms, ions, and clusters. 13 figs., 4 tabs

  18. Search for near-infrared counterparts of IRAS embedded sources in the M17 SW giant molecular cloud

    International Nuclear Information System (INIS)

    Elmegreen, D.M.; Phillips, J.; Beck, K.; Thomas, H.; Howard, J.

    1988-01-01

    Wide-field near-infrared and blue band plates of the region containing the M17 giant molecular cloud complex have been blinked to locate bright near-infrared stars that may be embedded in the M17 SW giant molecular cloud. Twenty such stars coincided with the positions of IRAS point sources that appeared embedded based on color-color diagrams. Some of these stars may be the sources of the infrared luminosities. Of the 20 stars, seven were too faint to appear on the B band plate. The optical magnitudes and colors determined from the plate image diameters were measured for the other 13 coincident stars; they are most likely upper main-sequence or pre-main-sequence stars with extinctions of 7 mag. The IRAS luminosity-temperature diagram indicates that the embedded sources in M17 are more massive than those in the Orion cloud. 35 references

  19. Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

    Directory of Open Access Journals (Sweden)

    Chad A. Stephenson

    2016-12-01

    Full Text Available Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germylmethane, or (H3Ge4C, followed by the design of a hybrid gas/solid-source molecular beam epitaxy system and subsequent growth of defect-free Ge1−xCx by molecular beam epitaxy (MBE. Secondary ion mass spectroscopy, transmission electron microscopy and contactless electroreflectance confirm the presence of carbon with very high crystal quality resulting in a decrease in the direct bandgap energy. This technique has broad applicability to growth of highly mismatched alloys by MBE.

  20. A source of translationally cold molecular beams

    Science.gov (United States)

    Sarkozy, Laszlo C.

    Currently the fields studying or using molecules with low kinetic energies are experiencing an unprecedented growth. Astronomers and chemists are interested in chemical reactions taking place at temperatures below or around 20 K, spectroscopists could make very precise measurements on slow molecules and molecular physicists could chart the potential energy surfaces more accurately. And the list continues. All of these experiments need slow molecules, with kinetic energies from around 10 cm-1 down to 0. Several designs of cold sources have already been made. The most interesting ones are presented. This work describes the design and the testing of a cold source based on the collisional cooling technique: the molecules of interest are cooled well below their freezing point by a precooled buffer gas. This way condensation is avoided. The source is a copper cell cooled to 4.2 K by an external liquid helium bath. The cell is filled with cold buffer gas (helium). The molecules of choice (ammonia) are injected through a narrow tube in the middle of the cell. The cold molecules leave the cell through a 1 millimeter hole. Two versions of pulsing techniques have been employed: a shutter blade which covers the source hole and opens it only for short moments, and a chopper that modulates the beam further downstream. Both produced pulse lengths around 1 millisecond. The source is tested in an experiment in which the emerging molecules are focused and detected. Time of flight technique is used to measure the kinetic energies. Two detectors have been employed: a microwave cavity to analyze the state of the molecules in the beam, and a mass spectrometer to measure the number density of the particles. The molecules coming out of the source hole are formed into a beam by an electrostatic quadrupole state selector. The quantum mechanical aspects and the elements of electrodynamics involved in the focusing are described. A computer simulation program is presented, which helped

  1. Further studies of the role of dense molecular clouds around outflow sources

    International Nuclear Information System (INIS)

    Verdes-Montenegro, L.; Torrelles, J.M.; Rodriguez, L.F.; Anglada, G.; Lopez, R.

    1989-01-01

    The (J,K) = (1,1) and (2,2) ammonia inversion transitions toward six regions with active star formation and evidence of gas outflows have been observed. Ammonia emission has been detected and mapped in five of these regions: AFGL 5142, AFGL 5157, AFGL 6366S, HHL 73, and S140N. NH3 (2,2) emission was detected toward the peak of the NH3 (1,1) core of AFGL 5157 and S140N. A rotational temperature of T(R) (2,2;1,1) = about 16 K was estimated for the two regions. Two new H2O masers of intense emission, S(nu) greater or equal 40 Jy, were detected toward the ammonia cores of AFGL 5142 and AFGL 5157. It is clear that the dense NH3 gas is closely associated with the star formation activities, since the ammonia cores in all peak close to the centers of activity. In particular, the AFGL 5157 ammonia condensation coincides with the geometrical center of a bipolar molecular outflow, suggesting that the exciting source is embedded in the ammonia core. In contrast, the molecular outflow in the AFGL 6366S region is located at the southeast edge of the NH3 condensation, suggesting that the exciting source is outside the ammonia core and that the morphology of the outflow may be influenced by the interaction with the dense ambient gas. 52 refs

  2. Hollow-anode plasma source for molecular beam epitaxy of gallium nitride

    International Nuclear Information System (INIS)

    Anders, A.; Newman, N.; Rubin, M.; Dickinson, M.; Jones, E.; Phatak, P.; Gassmann, A.

    1996-01-01

    GaN films have been grown by molecular beam epitaxy (MBE) using a hollow-anode nitrogen plasma source. The source was developed to minimize defect formation as a result of contamination and ion damage. The hollow-anode discharge is a special form of glow discharge with very small anode area. A positive anode voltage drop of 30 endash 40 V and an increased anode sheath thickness leads to ignition of a relatively dense plasma in front of the anode hole. Driven by the pressure gradient, the open-quote open-quote anode close-quote close-quote plasma forms a bright plasma jet streaming with supersonic velocity towards the substrate. Films of GaN have been grown on (0001) SiC and (0001) Al 2 O 3 at 600 endash 800 degree C. The films were investigated by photoluminescence, cathodoluminescence, x-ray diffraction, Rutherford backscattering, and particle-induced x-ray emission. The film with the highest structural quality had a rocking curve width of 5 arcmin, the lowest reported value for MBE growth to date. copyright 1996 American Institute of Physics

  3. Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

    Science.gov (United States)

    Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

    2015-03-15

    Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Sensitivity of molecular marker-based CMB models to biomass burning source profiles

    Science.gov (United States)

    Sheesley, Rebecca J.; Schauer, James J.; Zheng, Mei; Wang, Bo

    To assess the contribution of sources to fine particulate organic carbon (OC) at four sites in North Carolina, USA, a molecular marker chemical mass balance model (MM-CMB) was used to quantify seasonal contributions for 2 years. The biomass burning contribution at these sites was found to be 30-50% of the annual OC concentration. In order to provide a better understanding of the uncertainty in MM-CMB model results, a biomass burning profile sensitivity test was performed on the 18 seasonal composites. The results using reconstructed emission profiles based on published profiles compared well, while model results using a single source test profile resulted in biomass burning contributions that were more variable. The biomass burning contribution calculated using an average regional profile of fireplace emissions from five southeastern tree species also compared well with an average profile of open burning of pine-dominated forest from Georgia. The standard deviation of the results using different source profiles was a little over 30% of the annual average biomass contributions. Because the biomass burning contribution accounted for 30-50% of the OC at these sites, the choice of profile also impacted the motor vehicle source attribution due to the common emission of elemental carbon and polycyclic aromatic hydrocarbons. The total mobile organic carbon contribution was less effected by the biomass burning profile than the relative contributions from gasoline and diesel engines.

  5. Source-sink interaction: a century old concept under the light of modern molecular systems biology.

    Science.gov (United States)

    Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

    2017-07-20

    Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Design and synthesis of single-source molecular precursors to homogeneous multi-component oxide materials

    Science.gov (United States)

    Fujdala, Kyle Lee

    This dissertation describes the syntheses of single-source molecular precursors to multi-component oxide materials. These molecules possess a core metal or element with various combinations of -OSi(O tBu)3, -O2P(OtBu) 2, and -OB[OSi(OtBu)3] 2 ligands. Such molecules decompose under mild thermolytic conditions (models for oxide-supported metal species and multi-component oxides. Significantly, the first complexes to contain three or more heteroelements suitable for use in the TMP method have been synthesized. Compounds for use as single-source molecular precursors have been synthesized containing Al, B, Cr, Hf, Mo, V, W, and Zr, and their thermal transformations have been examined. Heterogeneous catalytic reactions have been examined for selected materials. Also, cothermolyses of molecular precursors and additional molecules (i.e., metal alkoxides) have been utilized to provide materials with several components for potential use as catalysts or catalyst supports. Reactions of one and two equivs of HOSi(OtBu) 3 with Cr(OtBu)4 afforded the first Cr(IV) alkoxysiloxy complexes (tBuO) 3CrOSi(OtBu)3 and ( tBuO)2Cr[OSi(OtBu) 3]2, respectively. The high-yielding, convenient synthesis of (tBuO)3CrOSi(O tBu)3 make this complex a useful single-source molecular precursor, via the TMP method, to Cr/Si/O materials. The thermal transformations of (tBuO)3CrOSi(O tBu)3 and (tBuO) 2Cr[OSi(OtBu)3]2 to chromia-silica materials occurr at low temperatures (≤180°C), to give isobutene as the major carbon-containing product. The material generated from the solid-state conversion of (tBuO) 3CrOSi(OtBu)3 (CrOS ss) has an unexpectedly high surface area of 315 m2 g-1 that is slightly reduced to 275 m2 g-1 after calcination at 500°C in O2. The xerogel obtained by the thermolysis of an n-octane solution of (tBuO)3CrOSi(O tBu)3 (CrOSixg) has a surface area of 315 m2 g-1 that is reduced to 205 m2 g-1 upon calcination at 500°C. Powder X-ray diffraction (PXRD) analysis revealed that Cr2O 3 is

  7. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

    Science.gov (United States)

    Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  8. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Khaled Taïbi

    2017-07-01

    Full Text Available Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  9. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    OpenAIRE

    Taïbi, Khaled; Campo, Antonio D. del; Vilagrosa Carmona, Alberto; Bellés, José M.; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J.; López-Nicolás, José M.; Mulet, José M.

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of pre...

  10. Isotopic and molecular fractionation in combustion; three routes to molecular marker validation, including direct molecular 'dating' (GC/AMS)

    Science.gov (United States)

    Currie, L. A.; Klouda, G. A.; Benner, B. A.; Garrity, K.; Eglinton, T. I.

    The identification of unique isotopic, elemental, and molecular markers for sources of combustion aerosol has growing practical importance because of the potential effects of fine particle aerosol on health, visibility and global climate. It is urgent, therefore, that substantial efforts be directed toward the validation of assumptions involving the use of such tracers for source apportionment. We describe here three independent routes toward carbonaceous aerosol molecular marker identification and validation: (1) tracer regression and multivariate statistical techniques applied to field measurements of mixed source, carbonaceous aerosols; (2) a new development in aerosol 14C metrology: direct, pure compound accelerator mass spectrometry (AMS) by off-line GC/AMS ('molecular dating'); and (3) direct observation of isotopic and molecular source emissions during controlled laboratory combustion of specific fuels. Findings from the combined studies include: independent support for benzo( ghi)perylene as a motor vehicle tracer from the first (statistical) and second (direct 'dating') studies; a new indication, from the third (controlled combustion) study, of a relation between 13C isotopic fractionation and PAH molecular fractionation, also linked with fuel and stage of combustion; and quantitative data showing the influence of both fuel type and combustion conditions on the yields of such species as elemental carbon and PAH, reinforcing the importance of exercising caution when applying presumed conservative elemental or organic tracers to fossil or biomass burning field data as in the first study.

  11. Molecular Ionization-Desorption Analysis Source (MIDAS) for Mass Spectrometry: Thin-Layer Chromatography

    Science.gov (United States)

    Winter, Gregory T.; Wilhide, Joshua A.; LaCourse, William R.

    2016-02-01

    Molecular ionization-desorption analysis source (MIDAS), which is a desorption atmospheric pressure chemical ionization (DAPCI) type source, for mass spectrometry has been developed as a multi-functional platform for the direct sampling of surfaces. In this article, its utility for the analysis of thin-layer chromatography (TLC) plates is highlighted. Amino acids, which are difficult to visualize without staining reagents or charring, were detected and identified directly from a TLC plate. To demonstrate the full potential of MIDAS, all active ingredients from an analgesic tablet, separated on a TLC plate, were successfully detected using both positive and negative ion modes. The identity of each of the compounds was confirmed from their mass spectra and compared against standards. Post separation, the chemical signal (blue permanent marker) as reference marks placed at the origin and solvent front were used to calculate retention factor (Rf) values from the resulting ion chromatogram. The quantitative capabilities of the device were exhibited by scanning caffeine spots on a TLC plate of increasing sample amount. A linear curve based on peak are, R2 = 0.994, was generated for seven spots ranging from 50 to 1000 ng of caffeine per spot.

  12. Crossed molecular beams

    International Nuclear Information System (INIS)

    Lee, Y.T.

    1976-01-01

    Research activities with crossed molecular beams at Lawrence Berkeley Laboratory during 1976 are described. Topics covered include: scattering of Ar*, Kr*, with Xe; metastable rare gas interactions, He* + H 2 ; an atomic and molecular halogen beam source; a crossed molecular beam study of the Cl + Br 2 → BrCl + Br reaction; O( 3 P) reaction dynamics, development of the high pressure plasma beam source; energy randomization in the Cl + C 2 H 3 Br → Br + C 2 H 3 Cl reaction; high resolution photoionization studies of NO and ICl; photoionization of (H 2 O)/sub n/ and (NH 3 ) 2 ; photoionization mass spectroscopy of NH 3 + and O 3 + ; photo fragmentation of bromine; and construction of chemiluminescence-laser fluorescence crossed molecular beam machine

  13. Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

    Science.gov (United States)

    Mather, Alison E; Vaughan, Timothy G; French, Nigel P

    2015-11-01

    Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis

    Science.gov (United States)

    Awad, A; Khalil, S. R; Abd-Elhakim, Y. M

    2015-01-01

    Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously. PMID:27175180

  15. Molecular line study of massive star-forming regions from the Red MSX Source survey

    Science.gov (United States)

    Yu, Naiping; Wang, Jun-Jie

    2014-05-01

    In this paper, we have selected a sample of massive star-forming regions from the Red MSX Source survey, in order to study star formation activities (mainly outflow and inflow signatures). We have focused on three molecular lines from the Millimeter Astronomy Legacy Team Survey at 90 GHz: HCO+(1-0), H13CO+(1-0) and SiO(2-1). According to previous observations, our sources can be divided into two groups: nine massive young stellar object candidates (radio-quiet) and 10 H II regions (which have spherical or unresolved radio emissions). Outflow activities have been found in 11 sources, while only three show inflow signatures in all. The high outflow detection rate means that outflows are common in massive star-forming regions. The inflow detection rate was relatively low. We suggest that this was because of the beam dilution of the telescope. All three inflow candidates have outflow(s). The outward radiation and thermal pressure from the central massive star(s) do not seem to be strong enough to halt accretion in G345.0034-00.2240. Our simple model of G318.9480-00.1969 shows that it has an infall velocity of about 1.8 km s-1. The spectral energy distribution analysis agrees our sources are massive and intermediate-massive star formation regions.

  16. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    Science.gov (United States)

    Krüger, Magnus; Huang, Mao-Dong; Becker-Roß, Helmut; Florek, Stefan; Ott, Ingo; Gust, Ronald

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of "fluorine as a probe in medicinal chemistry" an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells.

  17. Submicron particulate organic matter in the urban atmosphere: a new method for real-time measurement, molecular-level characterization and source apportionment

    Science.gov (United States)

    Müller, Markus; Eichler, Philipp; D'Anna, Barbara; Tan, Wen; Wisthaler, Armin

    2017-04-01

    We used a novel chemical analytical method for measuring submicron particulate organic matter in the atmosphere of three European cities (Innsbruck, Lyon, Valencia). Proton-Transfer-Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) was used in combination with the "chemical analysis of aerosol online" (CHARON) inlet for detecting particulate organic compounds on-line (i.e. without filter pre-collection), in real-time (1-min time resolution), at ng m-3 concentrations, with molecular-level resolution (i.e. obtaining molecular weight and elemental composition information). The CHARON-PTR-ToF-MS system monitored molecular tracers associated with different particle sources including levoglucosan from biomass combustion, PAHs from vehicular traffic, nicotine from cigarette smoking, and monoterpene oxidation products secondarily formed from biogenic emissions. The tracer information was used for interpreting positive matrix factorization (PMF) data which allowed us to apportion the sources of submicron particulate organic matter in the different urban environments. This work was funded through the PIMMS ITN, which was supported by the European Commission's 7th Framework Programme under grant agreement number 287382.

  18. CASMACAT

    DEFF Research Database (Denmark)

    Alabau, Vicent; Bonk, Ragnar; Buck, Christian

    2013-01-01

    We describe an open source workbench that offers advanced computer aided translation (CAT) functionality: post-editing machine translation (MT), interactive translation prediction (ITP), visualization of word alignment, extensive logging with replay mode, integration with eye trackers and e-pen....

  19. A ROTATING MOLECULAR DISK TOWARD IRAS 18162-2048, THE EXCITING SOURCE OF HH 80-81

    International Nuclear Information System (INIS)

    Fernandez-Lopez, M.; Curiel, S.; Girart, J. M.; Gomez, Y.; Ho, P. T. P.; Patel, N.

    2011-01-01

    We present several molecular line emission arcsecond and subarcsecond observations obtained with the Submillimeter Array in the direction of the massive protostar IRAS 18162-2048, the exciting source of HH 80-81. The data clearly indicate the presence of a compact (radius ∼425-850 AU) SO 2 structure, enveloping the more compact (radius ∼ sun . The SO 2 spectral line data also allow us to constrain the structure temperature between 120 and 160 K and the volume density ∼> 2 x 10 9 cm -3 . We also find that such a rotating flattened system could be unstable due to gravitational disturbances. The data from C 17 O line emission show a dense core within this star-forming region. Additionally, the H 2 CO and SO emissions appear clumpy and trace the disk-like structure, a possible interaction between a molecular core and the outflows, and in part, the cavity walls excavated by the thermal radio jet.

  20. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    International Nuclear Information System (INIS)

    Krüger, Magnus; Huang, Mao-Dong; Becker-Roß, Helmut; Florek, Stefan; Ott, Ingo; Gust, Ronald

    2012-01-01

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of “fluorine as a probe in medicinal chemistry” an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells. - Highlights: ► Development of HR-CS MAS for quantification of fluorine bound to organic molecules ► Measuring as molecular absorption of gallium monofluoride ► Quantification of organic-bound fluorine in biological material ► The concept of “fluorine as a probe in medicinal chemistry” could be established

  1. Parametrics for Molecular Deuterium Concentrations in the Source Region of the UW-IEC Device Using an Ion Acoustic Wave Diagnostic

    Science.gov (United States)

    Boris, D. R.; Emmert, G. A.

    2007-11-01

    The ion source region of the UW-Inertial Electrostatic Confinement device is comprised of a filament assisted DC discharge plasma that exists between the wall of the IEC vacuum chamber and the grounded spherical steel grid that makes up the anode of the IEC device. A 0-dimensional rate equation calculation of the molecular deuterium ion species concentration has been applied utilizing varying primary electron energy, and neutral gas pressure. By propagating ion acoustic waves in the source region of the IEC device the concentrations of molecular deuterium ion species have been determined for these varying plasma conditions, and high D3^+ concentrations have been verified. This was done by utilizing the multi-species ion acoustic wave dispersion relation, which relates the phase speed of the multi-species ion acoustic wave, vph, to the sum in quadrature of the concentration weighted ion acoustic sound speeds of the individual ion species.

  2. Using rapid diagnostic tests as source of malaria parasite DNA for molecular analyses in the era of declining malaria prevalence

    DEFF Research Database (Denmark)

    Ishengoma, Deus S; Lwitiho, Sudi; Madebe, Rashid A

    2011-01-01

    was conducted to examine if sufficient DNA could be successfully extracted from malaria rapid diagnostic tests (RDTs), used and collected as part of routine case management services in health facilities, and thus forming the basis for molecular analyses, surveillance and quality control (QC) testing of RDTs....... continued molecular surveillance of malaria parasites is important to early identify emerging anti-malarial drug resistance, it is becoming increasingly difficult to obtain parasite samples from ongoing studies, such as routine drug efficacy trials. To explore other sources of parasite DNA, this study...

  3. Molecular beam epitaxy growth of niobium oxides by solid/liquid state oxygen source and lithium assisted metal-halide chemistry

    Science.gov (United States)

    Tellekamp, M. Brooks; Greenlee, Jordan D.; Shank, Joshua C.; Doolittle, W. Alan

    2015-09-01

    In order to consistently grow high quality niobium oxides and lithium niobium oxides, a novel solid/liquid state oxygen source, LiClO4, has been implemented in a molecular beam epitaxy (MBE) system. LiClO4 is shown to decompose into both molecular and atomic oxygen upon heating. This allows oxidation rates similar to that of molecular oxygen but at a reduced overall beam flux, quantified by in situ Auger analysis. LiClO4 operation is decomposition limited to less than 400 °C, and other material limitations are identified. The design of a custom near-ambient NbCl5 effusion cell is presented, which improves both short and long term stability. Films of Nb oxidation state +2, +3, and +5 are grown using these new tools, including the multi-functional sub-oxide LiNbO2.

  4. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Krueger, Magnus [Freie Universitaet Berlin, Institut fuer Pharmazie, Pharmazeutische Chemie, Koenigin-Luise-Str. 2-4, 14195 Berlin (Germany); Huang, Mao-Dong; Becker-Ross, Helmut; Florek, Stefan [Leibniz Institut fuer Analytische Wissenschaften, ISAS-e.V., Department Berlin, Albert-Einstein-Str. 9, 12489 Berlin (Germany); Ott, Ingo [Technische Universitaet Carolo Wilhelmina zu Braunschweig, Institut fuer Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, 38106 Braunschweig (Germany); Gust, Ronald, E-mail: ronald.gust@uibk.ac.at [Universitaet Innsbruck, Institut fuer Pharmazie, Pharmazeutische Chemie, Innrain 80/82, 6020 Innsbruck (Austria)

    2012-03-15

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of 'fluorine as a probe in medicinal chemistry' an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells. - Highlights: Black-Right-Pointing-Pointer Development of HR-CS MAS for quantification of fluorine bound to organic molecules Black-Right-Pointing-Pointer Measuring as molecular absorption of gallium monofluoride Black-Right-Pointing-Pointer Quantification of organic-bound fluorine in biological material Black-Right-Pointing-Pointer The concept of 'fluorine as a probe in medicinal chemistry' could be established.

  5. Obtaining local reciprocal lattice vectors from finite-element analysis.

    Science.gov (United States)

    Sutter, John P; Connolley, Thomas; Hill, Tim P; Huang, Houcheng; Sharp, Doug W; Drakopoulos, Michael

    2008-11-01

    Finite-element analysis is frequently used by engineers at synchrotron beamlines to calculate the elastic deformation of a single crystal undergoing mechanical bending or thermal load. ANSYS Workbench software is widely used for such simulations. However, although ANSYS Workbench software provides useful information on the displacements, strains and stresses within the crystal, it does not yield the local reciprocal lattice vectors that would be required for X-ray diffraction calculations. To bridge this gap, a method based on the shape functions and interpolation procedures of the software itself has been developed. An application to the double-crystal bent Laue monochromator being designed for the I12 (JEEP) wiggler beamline at the Diamond Light Source is presented.

  6. Characterizing and sourcing ambient PM2.5 over key emission regions in China II: Organic molecular markers and CMB modeling

    Science.gov (United States)

    Zhou, Jiabin; Xiong, Ying; Xing, Zhenyu; Deng, Junjun; Du, Ke

    2017-08-01

    From November 2012 to July 2013, a sampling campaign was completed for comprehensive characterization of PM2.5 over four key emission regions in China: Beijing-Tianjin-Hebei (BTH), Yangzi River Delta (YRD), Pearl River Delta (PRD), and Sichuan Basin (SB). A multi-method approach, adopting different analytical and receptor modeling methods, was employed to determine the relative abundances of region-specific air pollution constituents and contributions of emission sources. This paper is focused on organic molecular marker based source apportionment using chemical mass balance (CMB) receptor modeling. Analyses of the organic molecular markers revealed that vehicle emission, coal combustion, biomass burning, meat cooking and natural gas combustion were the major contributors to organic carbon (OC) in PM2.5. The vehicle emission dominated the sources contributing to OC in spring at four sampling sites. During wintertime, the coal combustion had highest contribution to OC at BTH site, while the major source contributing to OC at YRD and PRD sites was vehicle emission. In addition, the relative contributions of different emission sources to PM2.5 mass at a specific location site and in a specific season revealed seasonal and spatial variations across all four sampling locations. The largest contributor to PM2.5 mass was secondary sulfate (14-17%) in winter at the four sites. The vehicle emission was found to be the major source (14-21%) for PM2.5 mass at PRD site. The secondary ammonium has minor variation (4-5%) across the sites, confirming the influences of regional emission sources on these sites. The distinct patterns of seasonal and spatial variations of source apportionment observed in this study were consistent with the findings in our previous paper based upon water-soluble ions and carbonaceous fractions. This makes it essential for the local government to make season- and region-specific mitigation strategies for abating PM2.5 pollution in China.

  7. The Molecular Level Characterization of Biodegradable Polymers Originated from Polyethylene Using Non-Oxygenated Polyethylene Wax as a Carbon Source for Polyhydroxyalkanoate Production.

    Science.gov (United States)

    Johnston, Brian; Jiang, Guozhan; Hill, David; Adamus, Grazyna; Kwiecień, Iwona; Zięba, Magdalena; Sikorska, Wanda; Green, Matthew; Kowalczuk, Marek; Radecka, Iza

    2017-08-28

    There is an increasing demand for bio-based polymers that are developed from recycled materials. The production of biodegradable polymers can include bio-technological (utilizing microorganisms or enzymes) or chemical synthesis procedures. This report demonstrates the corroboration of the molecular structure of polyhydroxyalkanoates (PHAs) obtained by the conversion of waste polyethylene (PE) via non-oxygenated PE wax (N-PEW) as an additional carbon source for a bacterial species. The N-PEW, obtained from a PE pyrolysis reaction, has been found to be a beneficial carbon source for PHA production with Cupriavidus necator H16. The production of the N-PEW is an alternative to oxidized polyethylene wax (O-PEW) (that has been used as a carbon source previously) as it is less time consuming to manufacture and offers fewer industrial applications. A range of molecular structural analytical techniques were performed on the PHAs obtained; which included nuclear magnetic resonance (NMR) and electrospray ionisation tandem mass spectrometry (ESI-MS/MS). Our study showed that the PHA formed from N-PEW contained 3-hydroxybutyrate (HB) with 11 mol% of 3-hydroxyvalerate (HV) units.

  8. Determination of total sulfur in agricultural samples by high-resolution continuum source flame molecular absorption spectrometry.

    Science.gov (United States)

    Virgilio, Alex; Raposo, Jorge L; Cardoso, Arnaldo A; Nóbrega, Joaquim A; Gomes Neto, José A

    2011-03-23

    The usefulness of molecular absorption was investigated for the determination of total sulfur (S) in agricultural samples by high-resolution continuum source flame molecular absorption spectrometry. The lines for CS at 257.595, 257.958, and 258.056 nm and for SH at 323.658, 324.064, and 327.990 nm were evaluated. Figures of merit, such as linear dynamic range, sensitivity, linear correlation, characteristic concentration, limit of detection, and precision, were established. For selected CS lines, wavelength-integrated absorbance equivalent to 3 pixels, analytical curves in the 100-2500 mg L(-1) (257.595 nm), 250-2000 mg L(-1) (257.958 nm), and 250-5000 mg L(-1) (258.056 nm) ranges with a linear correlation coefficient better than 0.9980 were obtained. Results were in agreement at a 95% confidence level (paired t test) with those obtained by gravimetry. Recoveries of S in fungicide and fertilizer samples were within the 84-109% range, and the relative standard deviation (n=12) was typically <5%.

  9. Investigation of natural phosphatidylcholine sources: separation and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2) of molecular species.

    Science.gov (United States)

    Le Grandois, Julie; Marchioni, Eric; Zhao, Minjie; Giuffrida, Francesca; Ennahar, Saïd; Bindler, Françoise

    2009-07-22

    This study is a contribution to the exploration of natural phospholipid (PL) sources rich in long-chain polyunsaturated fatty acids (LC-PUFAs) with nutritional interest. Phosphatidylcholines (PCs) were purified from total lipid extracts of different food matrices, and their molecular species were separated and identified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(2)). Fragmentation of lithiated adducts allowed for the identification of fatty acids linked to the glycerol backbone. Soy PC was particularly rich in species containing essential fatty acids, such as (18:2-18:2)PC (34.0%), (16:0-18:2)PC (20.8%), and (18:1-18:2)PC (16.3%). PC from animal sources (ox liver and egg yolk) contained major molecular species, such as (16:0-18:2)PC, (16:0-18:1)PC, (18:0-18:2)PC, or (18:0-18:1)PC. Finally, marine source (krill oil), which was particularly rich in (16:0-20:5)PC and (16:0-22:6)PC, appeared to be an interesting potential source for food supplementation with LC-PUFA-PLs, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).

  10. p-type ZnO films with solid-source phosphorus doping by molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Xiu, F.X.; Yang, Z.; Mandalapu, L.J.; Liu, J.L.; Beyermann, W. P.

    2006-01-01

    Phosphorus-doped p-type ZnO films were grown on r-plane sapphire substrates using molecular-beam epitaxy with a solid-source GaP effusion cell. X-ray diffraction spectra and reflection high-energy electron diffraction patterns indicate that high-quality single crystalline (1120) ZnO films were obtained. Hall and resistivity measurements show that the phosphorus-doped ZnO films have high hole concentrations and low resistivities at room temperature. Photoluminescence (PL) measurements at 8 K reveal a dominant acceptor-bound exciton emission with an energy of 3.317 eV. The acceptor energy level of the phosphorus dopant is estimated to be 0.18 eV above the valence band from PL spectra, which is also consistent with the temperature dependence of PL measurements

  11. Group III nitride-arsenide long wavelength lasers grown by elemental source molecular beam epitaxy

    International Nuclear Information System (INIS)

    Coldren, C. W.; Spruytte, S. G.; Harris, J. S.; Larson, M. C.

    2000-01-01

    Elemental source molecular beam epitaxy was used to grow InGaNAs quantum well samples, edge-emitting laser diodes, and vertical-cavity laser diodes on GaAs substrates. The quantum well samples exhibited an as-grown room temperature photoluminescence peak beyond 1310 nm which both increased dramatically in intensity and blueshifted with thermal annealing. Edge emitting laser diodes had threshold current densities as low as 450 and 750 A/cm 2 for single and triple quantum well active regions, respectively, and emitted light at 1220-1250 nm. The vertical cavity laser diodes emitted light at 1200 nm and had threshold current densities of 3 kA/cm 2 and efficiencies of 0.066 W/A. (c) 2000 American Vacuum Society

  12. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    Directory of Open Access Journals (Sweden)

    Yu-Hua Dean Fang

    2014-01-01

    Full Text Available Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC. Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.. Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita.

  13. Research Article Special Issue

    African Journals Online (AJOL)

    2017-09-10

    Sep 10, 2017 ... by providing users with various types of filtering and signal processing toolkits to extract ... Hence, NI-LabVIEW Biomedical Workbench with DAQ device can be one of the ..... GB camera only able to detect the remittance spectra from the skin su ..... using video imaging and blind source separation.

  14. Sources And Compositional Distribution Of Polycyclic Aromatic ...

    African Journals Online (AJOL)

    For molecular mass 178, an anthracene to anthracene plus phenanthrene ratio ≤ 0.10 was taken as indication of petroleum related sources, while a ratio > 0.10 indicated dominance of combustion related sources. For molecular mass 202, a fluoranthene to fluoranthene plus pyrene ratio ≤ 0.50 was indication of petroleum ...

  15. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Molecular Chemical Structure of Barley Proteins Revealed by Ultra-Spatially Resolved Synchrotron Light Sourced FTIR Microspectroscopy: Comparison of Barley Varieties

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    Barley protein structure affects the barley quality, fermentation, and degradation behavior in both humans and animals among other factors such as protein matrix. Publications show various biological differences among barley varieties such as Valier and Harrington, which have significantly different degradation behaviors. The objectives of this study were to reveal the molecular structure of barley protein, comparing various varieties (Dolly, Valier, Harrington, LP955, AC Metcalfe, and Sisler), and quantify protein structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling by using the ultra-spatially resolved synchrotron light sourced Fourier transform infrared microspectroscopy (SFTIRM). The items of the protein molecular structure revealed included protein structure α-helices, β-sheets, and others such as β-turns and random coils. The experiment was performed at the National Synchrotron Light Source in Brookhaven National Laboratory (BNL, US Department of Energy, NY). The results showed that with the SFTIRM, the molecular structure of barley protein could be revealed. Barley protein structures exhibited significant differences among the varieties in terms of proportion and ratio of model-fitted α-helices, β-sheets, and others. By using multi-component peaks modeling at protein amide I region of 1710-1576 cm -1 , the results show that barley protein consisted of approximately 18-34% of α-helices, 14-25% of β-sheets, and 44-69% others. AC Metcalfe, Sisler, and LP955 consisted of higher (P 0.05). The ratio of α-helices to others (0.3 to 1.0, P < 0.05) and that of β-sheets to others (0.2 to 0.8, P < 0.05) were different among the barley varieties. It needs to be pointed out that using a multi-peak modeling for protein structure analysis is only for making relative estimates and not exact determinations and only for the comparison purpose between varieties. The principal component analysis showed that protein amide I Fourier

  17. Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

    Science.gov (United States)

    Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

    2017-11-01

    Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.

  18. Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

    Science.gov (United States)

    Kowalewska, Zofia

    2011-07-01

    For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the ∆ν = 0 vibrational sequence within the electronic transition X 1∑ + → A 1П, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd xS y molecules. At the 258.056 nm line, with the wavelength range covering central pixel ± 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg -1 in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg -1 in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with sulphur content determined by X-ray fluorescence

  19. Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

    Energy Technology Data Exchange (ETDEWEB)

    Kowalewska, Zofia, E-mail: zofia.kowalewska@obr.pl

    2011-07-15

    For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the {Delta}{nu} = 0 vibrational sequence within the electronic transition X{sup 1}{Sigma}{sup +} {yields} A{sup 1}{Pi}, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd{sub x}S{sub y} molecules. At the 258.056 nm line, with the wavelength range covering central pixel {+-} 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg{sup -1} in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg{sup -1} in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with

  20. Growth kinetics and properties of ZnO/ZnMgO heterostructures grown by radical-source molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, S.V. [Institute of Semiconductor Technology, Technical University Braunschweig, Hans-Sommer-Str. 66, 38106 Braunschweig (Germany); Ioffe Physico-Technical Institute, Polytekhnicheskaya Street 26, 194021 St. Petersburg (Russian Federation); El-Shaer, A.; Bakin, A.; Waag, A. [Institute of Semiconductor Technology, Technical University Braunschweig, Hans-Sommer-Str. 66, 38106 Braunschweig (Germany); Shubina, T.V.; Listoshin, S.B. [Ioffe Physico-Technical Institute, Polytekhnicheskaya Street 26, 194021 St. Petersburg (Russian Federation)

    2007-07-01

    A phenomenological approach to quantitative description of Zn(Mg)O growth by radical-source molecular beam epitaxy, based on the experimental studies of RHEED intensity oscillations, has been developed. It allows a precise control of growth rate, composition and stoichiometry at any growth temperature, Along with optimization of a growth initiation procedure on a c-sapphire, it is necessary condition for fabrication of high quality ZnO epilayers and ZnO/ZnMgO heterostructures in a wide Mg composition range. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

    OpenAIRE

    Shahram Radei; F. Javier Carrión-Fité; Mònica Ardanuy; José María Canal

    2018-01-01

    This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin) using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100...

  2. Source Apportionment of Background PAHs in the Peace-Athabasca Delta (Alberta, Canada) Using Molecular Level Radiocarbon Analysis.

    Science.gov (United States)

    Jautzy, Josué J; Ahad, Jason M E; Hall, Roland I; Wiklund, Johan A; Wolfe, Brent B; Gobeil, Charles; Savard, Martine M

    2015-08-04

    The downstream accumulation of polycyclic aromatic hydrocarbons (PAHs) in the Peace-Athabasca Delta (PAD), an ecologically important landscape, is a key issue of concern given the rapid development of the oil sands industry in Northern Alberta, Canada. In addition to PAHs derived from industrial activity (i.e., oil sands mining) within the Athabasca watershed, however, forest fires and erosion of fossil fuel deposits within both the Athabasca and Peace watersheds are two potentially important natural sources of PAHs delivered to the PAD. Consequently, evaluating the environmental impact of mining activities requires a quantitative understanding of natural, background PAHs. Here, we utilize molecular-level natural-abundance radiocarbon measurements on an amalgamated sediment record from a Peace River flood-susceptible oxbow lake in the northern Peace sector of the PAD to quantitatively discriminate sources of naturally occurring alkylated PAHs (fossil and modern biomass). A radiocarbon mass balance quantified a predominantly natural petrogenic source (93% petrogenic, 7% forest fire) for alkylated PAHs during the past ∼50 years. Additionally, a significant petrogenic component determined for retene, a compound usually considered a biomarker for softwood combustion, suggests that its use as a unique forest fire indicator may not be suitable in PAD sediments receiving Peace watershed-derived fluvial inputs.

  3. Carbon sources in suspended particles and surface sediments from the Beaufort Sea revealed by molecular lipid biomarkers and compound-specific isotope analysis

    Directory of Open Access Journals (Sweden)

    I. Tolosa

    2013-03-01

    Full Text Available Molecular lipid biomarkers (hydrocarbons, alcohols, sterols and fatty acids and compound-specific isotope analysis of suspended particulate organic matter (SPM and surface sediments of the Mackenzie Shelf and slope (southeast Beaufort Sea, Arctic Ocean were studied in summer 2009. The concentrations of the molecular lipid markers, characteristic of known organic matter sources, were grouped and used as proxies to evaluate the relative importance of fresh algal, detrital algal, fossil, C3 terrestrial plants, bacterial and zooplankton material in the organic matter (OM of this area. Fossil and detrital algal contributions were the major fractions of the freshwater SPM from the Mackenzie River with ~34% each of the total molecular biomarkers. Fresh algal, C3 terrestrial, bacterial and zooplanktonic components represented much lower percentages, 17, 10, 4 and 80%, with a minor contribution of fossil and C3 terrestrial biomarkers. Characterization of the sediments revealed a major sink of refractory algal material mixed with some fresh algal material, fossil hydrocarbons and a small input of C3 terrestrial sources. In particular, the sediments from the shelf and at the mouth of the Amundsen Gulf presented the highest contribution of detrital algal material (60–75%, whereas those from the slope contained the highest proportion of fossil (40% and C3 terrestrial plant material (10%. Overall, considering that the detrital algal material is marine derived, autochthonous sources contributed more than allochthonous sources to the OM lipid pool. Using the ratio of an allochthonous biomarker (normalized to total organic carbon, TOC found in the sediments to those measured at the river mouth water, we estimated that the fraction of terrestrial material preserved in the sediments accounted for 30–40% of the total carbon in the inner shelf sediments, 17% in the outer shelf and Amundsen Gulf and up to 25% in the slope sediments. These estimates are low

  4. Dye shift: a neglected source of genotyping error in molecular ecology.

    Science.gov (United States)

    Sutton, Jolene T; Robertson, Bruce C; Jamieson, Ian G

    2011-05-01

    Molecular ecologists must be vigilant in detecting and accounting for genotyping error, yet potential errors stemming from dye-induced mobility shift (dye shift) may be frequently neglected and largely unknown to researchers who employ 3-primer systems with automated genotyping. When left uncorrected, dye shift can lead to mis-scoring alleles and even to falsely calling new alleles if different dyes are used to genotype the same locus in subsequent reactions. When we used four different fluorophore labels from a standard dye set to genotype the same set of loci, differences in the resulting size estimates for a single allele ranged from 2.07 bp to 3.68 bp. The strongest effects were associated with the fluorophore PET, and relative degree of dye shift was inversely related to locus size. We found little evidence in the literature that dye shift is regularly accounted for in 3-primer studies, despite knowledge of this phenomenon existing for over a decade. However, we did find some references to erroneous standard correction factors for the same set of dyes that we tested. We thus reiterate the need for strict quality control when attempting to reduce possible sources of genotyping error, and in cases where different dyes are applied to a single locus, perhaps mistakenly, we strongly discourage researchers from assuming generic correction patterns. © 2011 Blackwell Publishing Ltd.

  5. RF Wave Simulation Using the MFEM Open Source FEM Package

    Science.gov (United States)

    Stillerman, J.; Shiraiwa, S.; Bonoli, P. T.; Wright, J. C.; Green, D. L.; Kolev, T.

    2016-10-01

    A new plasma wave simulation environment based on the finite element method is presented. MFEM, a scalable open-source FEM library, is used as the basis for this capability. MFEM allows for assembling an FEM matrix of arbitrarily high order in a parallel computing environment. A 3D frequency domain RF physics layer was implemented using a python wrapper for MFEM and a cold collisional plasma model was ported. This physics layer allows for defining the plasma RF wave simulation model without user knowledge of the FEM weak-form formulation. A graphical user interface is built on πScope, a python-based scientific workbench, such that a user can build a model definition file interactively. Benchmark cases have been ported to this new environment, with results being consistent with those obtained using COMSOL multiphysics, GENRAY, and TORIC/TORLH spectral solvers. This work is a first step in bringing to bear the sophisticated computational tool suite that MFEM provides (e.g., adaptive mesh refinement, solver suite, element types) to the linear plasma-wave interaction problem, and within more complicated integrated workflows, such as coupling with core spectral solver, or incorporating additional physics such as an RF sheath potential model or kinetic effects. USDoE Awards DE-FC02-99ER54512, DE-FC02-01ER54648.

  6. System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management.

    Science.gov (United States)

    Kang, Wenjun; Kadri, Sabah; Puranik, Rutika; Wurst, Michelle N; Patil, Sushant A; Mujacic, Ibro; Benhamed, Sonia; Niu, Nifang; Zhen, Chao Jie; Ameti, Bekim; Long, Bradley C; Galbo, Filipo; Montes, David; Iracheta, Crystal; Gamboa, Venessa L; Lopez, Daisy; Yourshaw, Michael; Lawrence, Carolyn A; Aisner, Dara L; Fitzpatrick, Carrie; McNerney, Megan E; Wang, Y Lynn; Andrade, Jorge; Volchenboum, Samuel L; Furtado, Larissa V; Ritterhouse, Lauren L; Segal, Jeremy P

    2018-04-24

    Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory, a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. The System for Informatics in the Molecular Pathology Laboratory was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of the system, its clinical validation at the Genomic and Molecular Pathology Division at the University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing. Copyright © 2018. Published by Elsevier Inc.

  7. Molecular characterization of bacteriophages for microbial source tracking in Korea.

    Science.gov (United States)

    Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo

    2009-11-01

    We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

  8. Ion sources for accelerators

    International Nuclear Information System (INIS)

    Alton, G.D.

    1974-01-01

    A limited review of low charge sate positive and negative ion sources suitable for accelerator use is given. A brief discussion is also given of the concepts underlying the formation and extraction of ion beams. Particular emphasis is placed on the technology of ion sources which use solid elemental or molecular compounds to produce vapor for the ionization process

  9. HIERARCHICAL FRAGMENTATION OF THE ORION MOLECULAR FILAMENTS

    International Nuclear Information System (INIS)

    Takahashi, Satoko; Ho, Paul T. P.; Su, Yu-Nung; Teixeira, Paula S.; Zapata, Luis A.

    2013-01-01

    We present a high angular resolution map of the 850 μm continuum emission of the Orion Molecular Cloud-3 (OMC 3) obtained with the Submillimeter Array (SMA); the map is a mosaic of 85 pointings covering an approximate area of 6.'5 × 2.'0 (0.88 × 0.27 pc). We detect 12 spatially resolved continuum sources, each with an H 2 mass between 0.3-5.7 M ☉ and a projected source size between 1400-8200 AU. All the detected sources are on the filamentary main ridge (n H 2 ≥10 6 cm –3 ), and analysis based on the Jeans theorem suggests that they are most likely gravitationally unstable. Comparison of multi-wavelength data sets indicates that of the continuum sources, 6/12 (50%) are associated with molecular outflows, 8/12 (67%) are associated with infrared sources, and 3/12 (25%) are associated with ionized jets. The evolutionary status of these sources ranges from prestellar cores to protostar phase, confirming that OMC-3 is an active region with ongoing embedded star formation. We detect quasi-periodical separations between the OMC-3 sources of ≈17''/0.035 pc. This spatial distribution is part of a large hierarchical structure that also includes fragmentation scales of giant molecular cloud (≈35 pc), large-scale clumps (≈1.3 pc), and small-scale clumps (≈0.3 pc), suggesting that hierarchical fragmentation operates within the Orion A molecular cloud. The fragmentation spacings are roughly consistent with the thermal fragmentation length in large-scale clumps, while for small-scale cores it is smaller than the local fragmentation length. These smaller spacings observed with the SMA can be explained by either a helical magnetic field, cloud rotation, or/and global filament collapse. Finally, possible evidence for sequential fragmentation is suggested in the northern part of the OMC-3 filament.

  10. Emulation workbench for position sensitive gaseous scintillation detectors

    International Nuclear Information System (INIS)

    Pereira, L.; Margato, L.M.S.; Morozov, A.; Solovov, V.; Fraga, F. A. F.

    2015-01-01

    Position sensitive detectors based on gaseous scintillation proportional counters with Anger-type readout are being used in several research areas such as neutron detection, search for dark matter and neutrinoless double beta decay. Design and optimization of such detectors are complex and time consuming tasks. Simulations, while being a powerful tool, strongly depend on the light transfer models and demand accurate knowledge of many parameters, which are often not available. Here we describe an alternative approach based on the experimental evaluation of a detector using an isotropic point-like light source with precisely controllable light emission properties, installed on a 3D positioning system. The results obtained with the developed setup at validation conditions, when the scattered light is strongly suppressed show good agreement with simulations

  11. Molecular markers for use in plant molecular breeding and germplasm evaluation

    International Nuclear Information System (INIS)

    Edwards, J.D.; McCouch, S.R.

    2007-01-01

    A number of molecular marker technologies exist, each with different advantages and disadvantages. When available, genome sequence allows for the development of greater numbers and higher quality molecular markers. When genome sequence is limited in the organism of interest, related species may serve as sources of molecular markers. Some molecular marker technologies combine the discovery and assay of DNA sequence variations, and therefore can be used in species without the need for prior sequence information and up-front investment in marker development. As a prerequisite for marker-assisted selection (MAS), there must be a known association between genetic markers and genes affecting the phenotype to be modified. Comparative databases can facilitate the transfer of knowledge of genetic marker-phenotype association across species so that discoveries in one species may be applied to many others. Further genomics research and reductions in the costs associated with molecular markers will continue to provide new opportunities to employ MAS. (author)

  12. In silico carbon molecular beam epitaxial growth of graphene on the h-BN substrate: carbon source effect on van der Waals epitaxy

    Science.gov (United States)

    Lee, Jonghoon; Varshney, Vikas; Park, Jeongho; Farmer, Barry L.; Roy, Ajit K.

    2016-05-01

    Against the presumption that hexagonal boron-nitride (h-BN) should provide an ideal substrate for van der Waals (vdW) epitaxy to grow high quality graphene films, carbon molecular beam epitaxy (CMBE) techniques using solid carbon sublimation have reported relatively poor quality of the graphene. In this article, the CMBE growth of graphene on the h-BN substrate is numerically studied in order to identify the effect of the carbon source on the quality of the graphene film. The carbon molecular beam generated by the sublimation of solid carbon source materials such as graphite and glassy carbon is mostly composed of atomic carbon, carbon dimers and carbon trimers. Therefore, the graphene film growth becomes a complex process involving various deposition characteristics of a multitude of carbon entities. Based on the study of surface adsorption and film growth characteristics of these three major carbon entities comprising graphite vapour, we report that carbon trimers convey strong traits of vdW epitaxy prone to high quality graphene growth, while atomic carbon deposition is a surface-reaction limited process accompanied by strong chemisorption. The vdW epitaxial behaviour of carbon trimers is found to be substantial enough to nucleate and develop into graphene like planar films within a nanosecond of high flux growth simulation, while reactive atomic carbons tend to impair the structural integrity of the crystalline h-BN substrate upon deposition to form an amorphous interface between the substrate and the growing carbon film. The content of reactive atomic carbons in the molecular beam is suspected to be the primary cause of low quality graphene reported in the literature. A possible optimization of the molecular beam composition towards the synthesis of better quality graphene films is suggested.Against the presumption that hexagonal boron-nitride (h-BN) should provide an ideal substrate for van der Waals (vdW) epitaxy to grow high quality graphene films, carbon

  13. Separation of mouse testis cells on a Celsep (TM) apparatus and their usefulness as a source of high molecular weight DNA or RNA

    Science.gov (United States)

    Wolgemuth, D. J.; Gizang-Ginsberg, E.; Engelmyer, E.; Gavin, B. J.; Ponzetto, C.

    1985-01-01

    The use of a self-contained unit-gravity cell separation apparatus for separation of populations of mouse testicular cells is described. The apparatus, a Celsep (TM), maximizes the unit area over which sedimentation occurs, reduces the amount of separation medium employed, and is quite reproducible. Cells thus isolated have been good sources for isolation of DNA, and notably, high molecular weight RNA.

  14. Future Synchrotron Radiation Sources

    CERN Document Server

    Winick, Herman

    2003-01-01

    Sources of synchrotron radiation (also called synchrotron light) and their associated research facilities have experienced a spectacular growth in number, performance, and breadth of application in the past two to three decades. In 1978 there were eleven electron storage rings used as light sources. Three of these were small rings, all below 500 mega-electron volts (MeV), dedicated to this purpose; the others, with energy up to 5 giga-electron volts (GeV), were used parasitically during the operation of the ring for high energy physics research. In addition, at that time synchrotron radiation from nine cyclic electron synchrotrons, with energy up to 5 GeV, was also used parasitically. At present no cyclic synchrotrons are used, while about 50 electron storage rings are in operation around the world as fully dedicated light sources for basic and applied research in a wide variety of fields. Among these fields are structural molecular biology, molecular environmental science, materials, analytic chemistry, micr...

  15. InAs/GaAs quantum dot lasers with InGaP cladding layer grown by solid-source molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Yeh, N.-T.; Liu, W.-S.; Chen, S.-H.; Chiu, P.-C.; Chyi, J.-I.

    2002-01-01

    This letter presents the lasing properties of InAs/GaAs quantum dot lasers with InGaP cladding layers grown by solid-source molecular-beam epitaxy. These Al-free lasers exhibit a threshold current density of 138 A/cm 2 , an internal loss of 1.35 cm -1 , and an internal quantum efficiency of 31% at room temperature. At a low temperature, a very high characteristic temperature of 425 K and very low threshold current density of 30 A/cm 2 are measured

  16. Determination of phospholipids in soybean lecithin samples via the phosphorus monoxide molecule by high-resolution continuum source graphite furnace molecular absorption spectrometry.

    Science.gov (United States)

    Pires, Laís N; Brandão, Geovani C; Teixeira, Leonardo S G

    2017-06-15

    This paper presents a method for determining phospholipids in soybean lecithin samples by phosphorus determination using high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) via molecular absorption of phosphorus monoxide. Samples were diluted in methyl isobutyl ketone. The best conditions were found to be 213.561nm with a pyrolysis temperature of 1300°C, a volatilization temperature of 2300°C and Mg as a chemical modifier. To increase the analytical sensitivity, measurement of the absorbance signal was obtained by summing molecular transition lines for PO surrounding 213nm: 213.561, 213.526, 213.617 and 213.637nm. The limit of detection was 2.35mgg -1 and the precision, evaluated as relative standard deviation (RSD), was 2.47% (n=10) for a sample containing 2.2% (w/v) phosphorus. The developed method was applied for the analysis of commercial samples of soybean lecithin. The determined concentrations of phospholipids in the samples varied between 38.1 and 45% (w/v). Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Gas flow parameter determination by molecular beam method

    International Nuclear Information System (INIS)

    Zarvin, A.E.; Sharafutdinov, R.G.

    1977-01-01

    This paper describes a molecular-beam system intended for studying nonequilibrium processes in supersonic rarefied gas flows. The system represented is a small molecular beam source placed inside the low intensity wind tunnel of the Institute of Thermophysics, Siberian Branch of the USSR Academy of Sciences. The time-of-flight method is used for measuring molecular velocity distribution functions on molecular beam axis. (Auth.)

  18. New sources and instrumentation for neutrons in biology

    DEFF Research Database (Denmark)

    Teixeira, S. C. M.; Zaccai, G.; Ankner, J.

    2008-01-01

    Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.......Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed....

  19. CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Lagesen, Karin; Acar, Öncel

    2013-01-01

    This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats...

  20. Determination of sulfur in coal and ash slurry by high-resolution continuum source electrothermal molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Nakadi, Flávio V.; Rosa, Lilian R.; Veiga, Márcia A.M.S. da, E-mail: mamsveiga@ffclrp.usp.br

    2013-10-01

    We propose a procedure for the determination of sulfur in coal slurries by high resolution continuum source electrothermal molecular absorption spectrometry. The slurry, whose concentration is 1 mg mL{sup −1}, was prepared by mixing 50 mg of the sample with 5% v/v nitric acid and 0.04% m/v Triton X-100 and was homogenized manually. It sustained good stability. The determination was performed via CS molecular absorption at 257.592 nm, and the optimized vaporization temperature was 2500 °C. The accuracy of the method was ensured by analysis of certified reference materials SRM 1632b (trace elements in coal) and SRM 1633b (coal fly ash) from the National Institute of Standards and Technology, using external calibration with aqueous standards prepared in the same medium and used as slurry. We achieved good agreement with the certified reference materials within 95% confidence interval, LOD of 0.01% w/w, and RSD of 6%, which confirms the potential of the proposed method. - Highlights: • HR-CS ET MAS as a technique to determine sulfur in coal and ash • Utilization of (coal and coal fly ash) slurry as a sample preparation • Simple and fast method, which uses external calibration with aqueous standards without chemical modifier.

  1. Design and simulation of a circulating fluidized bed to clean the products of biomass gasification

    Energy Technology Data Exchange (ETDEWEB)

    Uchoa Neto, Moises; Carvalho, Yuri de Araujo [Dept. de Engenharia Mecanica. Faculdade de Tecnologia. Universidade de Brasilia, DF (Brazil); Oliveira, Taygoara Felamingo de; Barcelos, Manuel [Faculdade do Gama. Universidade de Brasilia, Gama, DF (Brazil)], e-mail: taygoara@unb.br

    2010-07-01

    The main goal of this work is to design a workbench circulating fluidized bed to study the cracking of tar in gases from the processes of biomass gasification. For this, a design methodology based on analytical results and empirical correlations for fluidized beds was employed. In parallel, a numerical code of open source technology (MFIX) for the solution of the transport equations of the multiphase flow in the column of a fluidized bed was used to give support to the choice of the design elements. The whole project of the workbench fluidized bed was completely developed, whose operation parameters such as bed geometry, gas velocity, circulating ratio and void fraction characterize a fast fluidization process. A preliminary mesh convergence study was executed with the numerical tool, that was validated comparing with analytical results. Among the most important results, the code computed the predicted value for the minimum fluidization. (author)

  2. Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  3. A double-stage pulsed discharge fluorine atom beam source

    International Nuclear Information System (INIS)

    Ren Zefeng; Qiu Minghui; Che Li; Dai Dongxu; Wang Xiuyan; Yang Xueming

    2006-01-01

    Molecular-beam intensity and speed ratio are two major limiting factors in many molecular-beam experiments. This article reports a high-intensity, high-speed-ratio, pulsed supersonic fluorine atom beam source using a double-stage discharge beam source. Its performance is indicated by the high-resolution time-of-flight spectrum in the crossed beam experiment of F( 2 P)+para-H 2

  4. CMG-biotools, a free workbench for basic comparative microbial genomics.

    Science.gov (United States)

    Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

    2013-01-01

    Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.

  5. Molecular detection of pathogens in water--the pros and cons of molecular techniques.

    Science.gov (United States)

    Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

    2010-08-01

    Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

  6. Determination of sulfur in food by high resolution continuum source flame molecular absorption spectrometry

    Science.gov (United States)

    Zambrzycka, Elżbieta; Godlewska-Żyłkiewicz, Beata

    2014-11-01

    In the present work, a fast, simple and sensitive analytical method for determination of sulfur in food and beverages by high resolution continuum source flame molecular absorption spectrometry was developed. The determination was performed via molecular absorption of carbon monosulfide, CS. Different CS rotational lines (257.959 nm, 258.033 nm, 258.055 nm), number of pixels and types of standard solution of sulfur, namely: sulfuric acid, sodium sulfate, ammonium sulfate, sodium sulfite, sodium sulfide, DL-cysteine, and L-cystine, were studied in terms of sensitivity, repeatability of results as well as limit of detection and limit of quantification. The best results were obtained for measurements of absorption of the CS molecule at 258.055 nm at the wavelength range covering 3 pixels and DL-cysteine in 0.2 mol L- 1 HNO3 solution as a calibration standard. Under optimized conditions the limit of detection and the limit of quantification achieved for sulfur were 10.9 mg L- 1 and 36.4 mg L- 1, respectively. The repeatability of the results expressed as relative standard deviation was typically beverage samples with added known amount of sulfur standard. The recovery of analyte from such samples was in the range of 93-105% with the repeatability in the range of 4.1-5.0%. The developed method was applied for the determination of sulfur in milk (194 ± 10 mg kg- 1), egg white (2188 ± 29 mg kg- 1), mineral water (31.0 ± 0.9 mg L- 1), white wine (260 ± 4 mg L- 1) and red wine (82 ± 2 mg L- 1), as well as in sample rich in ions, such as bitter mineral water (6900 ± 100 mg L- 1).

  7. A Problem-Solving Environment for Biological Network Informatics: Bio-Spice

    Science.gov (United States)

    2007-06-01

    user an environment to access software tools. The Dashboard is built upon the NetBeans Integrated Development Environment (IDE), an open source Java...based integration platform was demonstrated. During the subsequent six month development cycle, the first version of the NetBeans based Bio-SPICE...frameworks (OAA, NetBeans , and Systems Biology Workbench (SBW)[15]), it becomes possible for Bio-SPICE tools to truly interoperate. This interoperation

  8. Observations of far-infrared molecular emission lines from the Orion molecular cloud

    International Nuclear Information System (INIS)

    Viscuso, P.J.

    1986-01-01

    The Orion Nebula has been the subject of intensive study for over one hundred years. Far-infrared (FIR) molecular line observations of CO in the shock region surrounding the infrared source IRc2 have suggested that the molecular hydrogen density in the shocked and post-shock gas is roughly 3 x 10 6 cm -3 . The temperature of this gas is on the order of 750-2000K. IRc2, like other nearby infrared sources within the Nebula, is thought to be a site of recent star formation. This object is apparently at the center of a massive bipolar molecular outflow of gas, which is producing a shock front where it meets the ambient molecular cloud surrounding IRc2. Study of such regions is important for the understanding of the chemical and physical processes that are involved in the formation of stars from molecular clouds. Recently, several far-infrared transitions among the low-lying levels of OH have been observed toward IRc2. OH is thought to be abundant, and it plays an important role in the chemical evolution of the shock and post-shock regions. The OH emission serves as a sensitive probe of the temperature and density for the shock-processed gas. A rigorous treatment of the radiative transfer of these measured transitions is performed using the escape probability formalism. From this analysis, the author determines the temperature of the OH-emitting region to be on the order of 40K. This suggests that the gas is part of the post-shock gas that has cooled sufficiently, most likely by way of radiative cooling by CO

  9. Soft X-Ray Microscopy and Spectroscopy at the Molecular Environmental Science Beamline at the Advanced Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Bluhm, Hendrik; Andersson, Klas J.; Araki, Tohru; Benzerara, Karim; Brown, Gordon E.; Dynes, Jay J.; Ghosal, Sutapa; Gilles, Mary K.; Hansen, Hans C.; Hemminger, J. C.; Hitchcock, Adam P.; Ketteler, Guido; Kilcoyne, Arthur L.; Kneedler, Eric M.; Lawrence, John R.; Leppard, Gary G.; Majzlam, Juraj; Mun, B. S.; Myneni, Satish C.; Nilsson, Anders R.; Ogasawara, Hirohito; Ogletree, D. F.; Pecher, Klaus H.; Salmeron, Miquel B.; Shuh, David K.; Tonner, Brian; Tyliszczak, Tolek; Warwick, Tony; Yoon, T. H.

    2006-02-01

    We present examples of the application of synchrotron-based spectroscopies and microscopies to environmentally-relevant samples. The experiments were performed at the Molecular Environmental Science beamline (11.0.2) at the Advanced Light Source, Lawrence Berkeley National Laboratory. Examples range from the study of water monolayers on Pt(111) single crystal surfaces using X-ray emission spectroscopy and the examination of alkali halide solution/water vapor interfaces using ambient pressure photoemission spectroscopy, to the investigation of actinides, river-water biofilms, Al-containing colloids and mineral-bacteria suspensions using scanning transmission X-ray spectromicroscopy. The results of our experiments show that spectroscopy and microscopy in the soft X-ray energy range are excellent tools for the investigation of environmentally relevant samples under realistic conditions, i.e. with water or water vapor present at ambient temperature.

  10. Wood burning pollution in southern Chile: PM2.5 source apportionment using CMB and molecular markers.

    Science.gov (United States)

    Villalobos, Ana M; Barraza, Francisco; Jorquera, Héctor; Schauer, James J

    2017-06-01

    Temuco is a mid-size city representative of severe wood smoke pollution in southern Chile; i.e., ambient 24-h PM 2.5 concentrations have exceeded 150 μg/m 3 in the winter season and the top concentration reached 372 μg/m 3 in 2010. Annual mean concentrations have decreased but are still above 30 μg/m 3 . For the very first time, a molecular marker source apportionment of ambient organic carbon (OC) and PM 2.5 was conducted in Temuco. Primary resolved sources for PM 2.5 were wood smoke (37.5%), coal combustion (4.4%), diesel vehicles (3.3%), dust (2.2%) and vegetative detritus (0.7%). Secondary inorganic PM 2.5 (sulfates, nitrates and ammonium) contributed 4.8% and unresolved organic aerosols (generated from volatile emissions from incomplete wood combustion), including secondary organic aerosols, contributed 47.1%. Adding the contributions of unresolved organic aerosols to those from primary wood smoke implies that wood burning is responsible for 84.6% of the ambient PM 2.5 in Temuco. This predominance of wood smoke is ultimately due to widespread poverty and a lack of efficient household heating methods. The government has been implementing emission abatement policies but achieving compliance with ambient air quality standards for PM 2.5 in southern Chile remains a challenge. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. A combined thermal dissociation and electron impact ionization source for RIB generation

    International Nuclear Information System (INIS)

    Alton, G.D.; Williams, C.

    1995-01-01

    The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for RIB applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility (HRIBF), now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article

  12. Determination of boron isotope ratios by high-resolution continuum source molecular absorption spectrometry using graphite furnace vaporizers

    Science.gov (United States)

    Abad, Carlos; Florek, Stefan; Becker-Ross, Helmut; Huang, Mao-Dong; Heinrich, Hans-Joachim; Recknagel, Sebastian; Vogl, Jochen; Jakubowski, Norbert; Panne, Ulrich

    2017-10-01

    Boron isotope amount ratios n(10B)/n(11B) have been determined by monitoring the absorption spectrum of boron monohydride (BH) in a graphite furnace using high-resolution continuum source molecular absorption spectrometry (HR-CS-MAS). Bands (0 → 0) and (1 → 1) for the electronic transition X1Σ+ → A1Π were evaluated around wavelengths 433.1 nm and 437.1 nm respectively. Clean and free of memory effect molecular spectra of BH were recorded. In order to eliminate the memory effect of boron, a combination of 2% (v/v) hydrogen gas in argon and 1% trifluoromethane in argon, an acid solution of calcium chloride and mannitol as chemical modifiers was used. Partial least square regression (PLS) for analysis of samples and reference materials were applied. For this, a spectral library with different isotopes ratios for PLS regression was built. Results obtained around the 433.1 nm and 437.1 nm spectral regions are metrologically compatible with those reported by mass spectrometric methods. Moreover, for the evaluated region of 437 nm, an accuracy of 0.15‰ is obtained as the average deviation from the isotope reference materials. Expanded uncertainties with a coverage factor of k = 2 range between 0.15 and 0.44‰. This accuracy and precision are compatible with those obtained by mass spectrometry for boron isotope ratio measurements.

  13. Cell_motility: a cross-platform, open source application for the study of cell motion paths

    Directory of Open Access Journals (Sweden)

    Gevaert Kris

    2006-06-01

    Full Text Available Abstract Background Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s used. Results We here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at http://genesis.UGent.be/cell_motility . Conclusion In providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient

  14. Relationship between THMs/NDMA formation potential and molecular weight of organic compounds for source and treated water in Shanghai, China.

    Science.gov (United States)

    An, Dong; Gu, Bin; Sun, Sainan; Zhang, Han; Chen, Yanan; Zhu, Huifeng; Shi, Jian; Tong, Jun

    2017-12-15

    Molecular weight (MW) distributions in source and treated water in Shanghai, China were investigated to understand the relationship between trihalomethanes formation potential/N-nitrosodimethylamine formation potential (THMFP/NDMAFP) and dissolved organic carbon (DOC) for different MW ranges (30KDa). The result of MW distributions in source water indicated a relationship between THMFP/NDMAFP and DOC such that DOC for 30KDa THMFP was totally removed whereas NDMA according to the results for treated water between DOC and NDMAFP (R 2 =0.94 and 0.93 for sand and GAC filtration, respectively). The results may provide researchers with targeted treatment strategies to destroy, remove, or reduce the occurrence of THMs and NDMA precursors. The findings presented in this study will be of great value in future work for selecting suitable drinking water treatment processes to minimize the formation of disinfection by-products using chlorine or chloramine disinfection. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Contribution to the study of the molecular scattering of light. Use of a laser as light source (1963)

    International Nuclear Information System (INIS)

    Slama, L.

    1963-01-01

    The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [fr

  16. Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.

    Science.gov (United States)

    Beckers, Matthew; Mohorianu, Irina; Stocks, Matthew; Applegate, Christopher; Dalmay, Tamas; Moulton, Vincent

    2017-06-01

    Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this. © 2017 Beckers et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  17. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  18. Molecular ion photofragment spectroscopy

    International Nuclear Information System (INIS)

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O 2 + ( 4 π/sub u/) metastable state which is found to consist of two main components: the 4 π/sub 5/2/ and 4 π/sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the 4 π/sub 3/2/ and 4 π/sub 1/2/ spin components having a short lifetime (approx. 6 ms)

  19. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  20. The apparel industry in West Europe

    OpenAIRE

    Hilger, Jan

    2009-01-01

    The Apparel Industry was one of the first globally operating industries. Already in the early 1970ies did European fashion companies extend their manufacturing workbenches into lower cost neighbouring countries, making it one of the first industries to have a globally distributed network. In the first decade of the 21st century, the conditions for clothes manufacturing has changed considerably. The Sourcing Share of Asia increased dramatically especially since Chinas partici...

  1. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    International Nuclear Information System (INIS)

    Shirley, Yancy L.; Svoboda, Brian; Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John; Rosolowsky, Erik; Gerner, Thomas; Mairs, Steven; Dunham, Miranda K.

    2013-01-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg 2 . We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO + and N 2 H + 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N 2 H + 3-2 emission (T mb > 0.5 K) without HCO + 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO + is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s –1 consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH 3 observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N 2 H + than HCO + integrated intensity, but we find no correlations between the N 2 H + /HCO + ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  2. Tuned sources of submillimetre radiation

    International Nuclear Information System (INIS)

    Berezhnyj, V.L.

    1981-01-01

    The main present directions of development of sources of frequency coherent tuned radiation of electromagnetic waves in the submillimeter range: nonlinear mixing of different frequencies; semiconductor lasers; molecular lasers with optical pumping; relativistic electron beams in a magnetic field as submillimeter radiation sources; submillimeter radiation sources on the basis of SHF classical electrovacuum devices - are considered. The designs of generator systems and their specifications are presented. The main parameters of electromagnetic radiation of different sources, such as: power, stability, frequency, tuning range - are presented. The methods of improving sources and electromagnetic radiation parameters are proposed. The examples of possible applications of submillimeter radiation in different spheres of science and technology are given [ru

  3. Molecular Diagnostics of the Interstellar Medium and Star Forming Regions

    Science.gov (United States)

    Hartquist, T. W.; Dalgarno, A.

    1996-03-01

    Selected examples of the use of observationally inferred molecular level populations and chemical compositions in the diagnosis of interstellar sources and processes important in them (and in other diffuse astrophysical sources) are given. The sources considered include the interclump medium of a giant molecular cloud, dark cores which are the progenitors of star formation, material responding to recent star formation and which may form further stars, and stellar ejecta (including those of supernovae) about to merge with the interstellar medium. The measurement of the microwave background, mixing of material between different nuclear burning zones in evolved stars and turbulent boundary layers (which are present in and influence the structures and evolution of all diffuse astrophysical sources) are treated.

  4. Determination of sulfur in food by high resolution continuum source flame molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zambrzycka, Elżbieta; Godlewska-Żyłkiewicz, Beata, E-mail: bgodlew@uwb.edu.pl

    2014-11-01

    In the present work, a fast, simple and sensitive analytical method for determination of sulfur in food and beverages by high resolution continuum source flame molecular absorption spectrometry was developed. The determination was performed via molecular absorption of carbon monosulfide, CS. Different CS rotational lines (257.959 nm, 258.033 nm, 258.055 nm), number of pixels and types of standard solution of sulfur, namely: sulfuric acid, sodium sulfate, ammonium sulfate, sodium sulfite, sodium sulfide, DL-cysteine, and L-cystine, were studied in terms of sensitivity, repeatability of results as well as limit of detection and limit of quantification. The best results were obtained for measurements of absorption of the CS molecule at 258.055 nm at the wavelength range covering 3 pixels and DL-cysteine in 0.2 mol L{sup −1} HNO{sub 3} solution as a calibration standard. Under optimized conditions the limit of detection and the limit of quantification achieved for sulfur were 10.9 mg L{sup −1} and 36.4 mg L{sup −1}, respectively. The repeatability of the results expressed as relative standard deviation was typically < 5%. The accuracy of the method was tested by analysis of digested biological certified reference materials (soya bean flour, corn flour and herbs) and recovery experiment for beverage samples with added known amount of sulfur standard. The recovery of analyte from such samples was in the range of 93–105% with the repeatability in the range of 4.1–5.0%. The developed method was applied for the determination of sulfur in milk (194 ± 10 mg kg{sup −1}), egg white (2188 ± 29 mg kg{sup −1}), mineral water (31.0 ± 0.9 mg L{sup −1}), white wine (260 ± 4 mg L{sup −1}) and red wine (82 ± 2 mg L{sup −1}), as well as in sample rich in ions, such as bitter mineral water (6900 ± 100 mg L{sup −1}). - Highlights: • HR-CS FMAS technique was used for sulfur measurement via molecular absorption of carbon monosulfide, CS. • Organic DL

  5. MoleculeNet: a benchmark for molecular machine learning.

    Science.gov (United States)

    Wu, Zhenqin; Ramsundar, Bharath; Feinberg, Evan N; Gomes, Joseph; Geniesse, Caleb; Pappu, Aneesh S; Leswing, Karl; Pande, Vijay

    2018-01-14

    Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

  6. Determination of sulfur in bovine serum albumin and L-cysteine using high-resolution continuum source molecular absorption spectrometry of the CS molecule

    Science.gov (United States)

    Andrade-Carpente, Eva; Peña-Vázquez, Elena; Bermejo-Barrera, Pilar

    2016-08-01

    In this study, the content of sulfur in bovine serum albumin and L-cysteine was determined using high-resolution continuum source molecular absorption spectrometry of the CS molecule, generated in a reducing air-acetylene flame. Flame conditions (height above the burner, measurement time) were optimized using a 3.0% (v/v) sulfuric acid solution. A microwave lab station (Ethos Plus MW) was used for the digestion of both compounds. During the digestion step, sulfur was converted to sulfate previous to the determination. Good repeatability (4-10%) and analytical recovery (91-106%) was obtained.

  7. 3Dmol.js: molecular visualization with WebGL.

    Science.gov (United States)

    Rego, Nicholas; Koes, David

    2015-04-15

    3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

  8. Determination of trace concentrations of chlorine in aqueous solutions by high-resolution continuum source graphite furnace molecular absorption spectrometry

    Science.gov (United States)

    Machyňák, Ľubomír; Čacho, František; Němeček, Martin; Beinrohr, Ernest

    2016-11-01

    Trace concentrations of total chlorine were determined by means of molecular absorption of indium mono-chloride (InCl) at 267.217 nm using high-resolution continuum source graphite furnace molecular absorption spectrometry. The effects of chemical modifiers and the amount of In on the sensitivity and accuracy were investigated. The optimum pyrolysis and vaporization temperatures were 600 °C and 1400 °C, respectively. The limit of detection and characteristic mass were found to be 0.10 ng and 0.21 ng, respectively. Potential non-spectral and spectral interferences were tested for various metals and non-metals at concentrations up to 50 mg L- 1 and for phosphoric, sulphuric and nitric acids. No spectral interferences were observed. Significant non-spectral interferences were observed with F, Br, and I at concentrations higher than 1 mg L- 1, 5 mg L- 1 and 25 mg L- 1, respectively, which is probably caused by formation of competitive indium halogen molecules. Higher concentrations of mineral acids depressed the signal owing to the formation of volatile HCl. The calibration curve was linear in the range between 0.3 and 10 ng with a correlation coefficient of R = 0.993. The elaborated method was used for the chlorine determination in various waters and a drug sample.

  9. Preparation and electrical properties of boron and boron phosphide films obtained by gas source molecular beam deposition

    Energy Technology Data Exchange (ETDEWEB)

    Kumashiro, Y.; Yokoyama, T.; Sakamoto, T.; Fujita, T. [Yokohama National Univ. (Japan)

    1997-10-01

    Boron and boron phosphide films were prepared by gas source molecular beam deposition on sapphire crystal at various substrate temperatures up to 800{degrees}C using cracked B{sub 2}H{sub 6} (2% in H{sub 2}) at 300{degrees}C and cracked PH{sub 3} (20% in H{sub 2}) at 900{degrees}C. The substrate temperatures and gas flow rates of the reactant gases determined the film growth. The boron films with amorphous structure are p type. Increasing growth times lead to increasing mobilities and decreasing carrier concentrations. Boron phosphide film with maximum P/B ratio is obtained at a substrate temperature of 600{degrees}C, below and above which they become phosphorous deficient due to insufficient supply of phosphorus and thermal desorption of the phosphorus as P{sub 2}, respectively, but they are all n type conductors due to phosphorus vacancies.

  10. Photoelectron spectroscopy of supersonic molecular beams

    International Nuclear Information System (INIS)

    Pollard, J.E.; Trevor, D.J.; Lee, Y.T.; Shirley, D.A.

    1981-01-01

    A high-resolution photoelectron spectrometer which uses molecular beam sampling is described. Photons from a rare-gas resonance lamp or UV laser are crossed with the beam from a differentially pumped supersonic nozzle source. The resulting photoelectrons are collected by an electrostatic analyzer of a unique design consisting of a 90 0 spherical sector preanalyzer, a system of lenses, and a 180 0 hemispherical deflector. A multichannel detection system based on dual microchannel plates with a resistive anode position encoder provides an increase in counting efficiency by a factor of 12 over the equivalent single channel detector. The apparatus has demonstrated an instrumental resolution of better than 10 meV FWHM, limited largely by the photon source linewidth. A quadrupole mass spectrometer is used to characterize the composition of the molecular beam. Extensive differential pumping is provided to protect the critical surfaces of the analyzer and mass spectrometer from contamination. Because of the near elimination of Doppler and rotational broadenings, the practical resolution is the highest yet obtained in molecular PES

  11. A new storage-ring light source

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Alex [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-06-01

    A recently proposed technique in storage ring accelerators is applied to provide potential high-power sources of photon radiation. The technique is based on the steady-state microbunching (SSMB) mechanism. As examples of this application, one may consider a high-power DUV photon source for research in atomic and molecular physics or a high-power EUV radiation source for industrial lithography. A less challenging proof-of-principle test to produce IR radiation using an existing storage ring is also considered.

  12. Guidelines on the use of molecular genetics in reintroduction programs

    Science.gov (United States)

    Michael K. Schwartz

    2005-01-01

    The use of molecular genetics can play a key role in reintroduction efforts. Prior to the introduction of any individuals, molecular genetics can be used to identify the most appropriate source population for the reintroduction, ensure that no relic populations exist in the reintroduction area, and guide captive breeding programs. The use of molecular genetics post-...

  13. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    Energy Technology Data Exchange (ETDEWEB)

    Shirley, Yancy L.; Svoboda, Brian [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John [CASA, University of Colorado, CB 389, Boulder, CO 80309 (United States); Rosolowsky, Erik [Department of Physics, University of Alberta, 4-181 CCIS Edmonton AB T6G 2E1 (Canada); Gerner, Thomas [Max-Planck-Institut für Astronomie (MPIA), Knigstuhl 17, D-69117 Heidelberg (Germany); Mairs, Steven [Department of Physics and Astronomy, University of Victoria, P.O. Box 3055, STN CSC, Victoria, BC V8W 3P6 (Canada); Dunham, Miranda K. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520 (United States)

    2013-11-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg{sup 2}. We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO{sup +} and N{sub 2}H{sup +} 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N{sub 2}H{sup +} 3-2 emission (T {sub mb} > 0.5 K) without HCO{sup +} 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO{sup +} is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s{sup –1} consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH{sub 3} observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N{sub 2}H{sup +} than HCO{sup +} integrated intensity, but we find no correlations between the N{sub 2}H{sup +}/HCO{sup +} ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  14. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    Science.gov (United States)

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  15. Agent Based Reasoning in Multilevel Flow Modeling

    DEFF Research Database (Denmark)

    Lind, Morten; Zhang, Xinxin

    2012-01-01

    to launch the MFM Workbench into an agent based environment, which can complement disadvantages of the original software. The agent-based MFM Workbench is centered on a concept called “Blackboard System” and use an event based mechanism to arrange the reasoning tasks. This design will support the new...

  16. Molecular beam kinetics

    International Nuclear Information System (INIS)

    Behrens, R. Jr.

    1975-11-01

    The design of a crossed molecular beam ''supermachine'' for neutral--neutral collisions is discussed. The universal electron bombardment ionizer, mass filter, and ion detection system of the detector, the supersonic nozzle sources, the differential pumping arrangement for the sources and detector, the time-of-flight detection of scattered products, and the overall configuration of the apparatus are described. The elastic scattering of two systems, CH 4 + Ar and NH 3 + Ar, has been measured using the supermachine with two supersonic nozzle sources. The rainbow structure and the interference oscillations are seen in each system. The best fit to the data was found using a Morse--Spline--Van der Waals (MSV) potential. The three potential parameters epsilon, r/sub m/, and β were found to be 2.20(+-0.04) x 10 -14 ergs, 3.82(+-0.04)A, and 7.05 +- 0.20 for CH 4 + Ar, and 2.21(+-0.04) x 10 -14 ergs 3.93 (+-0.05)A, and 8.45 +- 0.30 for NH 3 + Ar. A new phenomenon in crossed molecular beams of condensation of a molecule on a cluster to form a complex was observed. A bromine molecule condensed on clusters of chlorine (Cl 2 )/sub chi/ and ammonia (NH 3 )/sub chi/. The value of chi for measurements in these experiments ranges from 7 to 40 for chlorine clusters and from 10 to 70 ammonia clusters

  17. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

    Science.gov (United States)

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

  18. Molten Fluoride Salts as Fluorine Source in the Production of Molecular Sidebands

    CERN Document Server

    Shoaib, Maryam

    2015-01-01

    The medically important isotopes Yttrium and Zirconium were selected for fluorination. After this, 30 $\\mu$g of NaF as fluorine source was put in mass marker in the target unit. It was heated and plasma ion source was used to ionize the vapors. The ion source efficiency was 27\\%. It was observed that the yield for fluorine was not enough for various mass marker temperatures (0 A - 40 A) and ion source temperatures (2000 $^{o}$C - 2150$^{o}$C) to be reacted with other elements. The optimum temperatures of mass marker was observed here as 35 A. The project can be proceeded for further high temperatures and for different fluorine sources.

  19. ``Making the Molecular Movie'': First Frames

    Science.gov (United States)

    Miller, R. J. Dwayne

    2011-03-01

    Femtosecond Electron Diffraction has enabled atomic resolution to structural changes as they occur, essentially watching atoms move in real time--directly observe transition states. This experiment has been referred to as ``making the molecular movie'' and has been previously discussed in the context of a gedanken experiment. With the recent development of femtosecond electron pulses with sufficient number density to execute single shot structure determinations, this experiment has been finally realized. A new concept in electron pulse generation was developed based on a solution to the N-body electron propagation problem involving up to 10,000 interacting electrons that has led to a new generation of extremely bright electron pulsed sources that minimizes space charge broadening effects. Previously thought intractable problems of determining t=0 and fully characterizing electron pulses on the femtosecond time scale have now been solved through the use of the laser pondermotive potential to provide a time dependent scattering source. Synchronization of electron probe and laser excitation pulses is now possible with an accuracy of 10 femtoseconds to follow even the fastest nuclear motions. The camera for the ``molecular movie'' is well in hand based on high bunch charge electron sources. Several movies depicting atomic motions during passage through structural transitions will be shown. Atomic level views of the simplest possible structural transition, melting, will be presented for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated to the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron systems will be presented in which an exceptionally cooperative phase transitions has been observed. The primitive origin of molecular

  20. High temperature and high resolution uv photoelectron spectroscopy using supersonic molecular beams

    International Nuclear Information System (INIS)

    Wang, Lai-Sheng; Reutt-Robey, J.E.; Niu, B.; Lee, Y.T.; Shirley, D.A.

    1989-07-01

    A high temperature molecular beam source with electron bombardment heating has been built for high resolution photoelectron spectroscopic studies of high temperature species and clusters. This source has the advantages of: producing an intense, continuous, seeded molecular beam, eliminating the interference of the heating mechanism from the photoelectron measurement. Coupling the source with our hemispherical electron energy analyzer, we can obtain very high resolution HeIα (584 angstrom) photoelectron spectra of high temperature species. Vibrationally-resolved photoelectron spectra of PbSe, As 2 , As 4 , and ZnCl 2 are shown to demonstrate the performance of the new source. 25 refs., 8 figs., 1 tab

  1. A combined thermal dissociation and electron impact ionization source for radioactive ion beam generationa

    International Nuclear Information System (INIS)

    Alton, G.D.; Williams, C.

    1996-01-01

    The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. copyright 1996 American Institute of Physics

  2. A photoionization study of hydrogen-bound clusters in a supersonic molecular beam

    International Nuclear Information System (INIS)

    Cook, K.D.; Jones, G.G.; Taylor, J.W.

    1980-01-01

    Hydrogen bonding of methanol, methanol-d, ethanol, and trifluoroethanol is investigated with a supersonic molecular beam as a sampling system for a photoionization quadrupole mass spectrometer. Monochromatized vacuum ultraviolet synchrotron radiation is used as the ionizing source. Cluster ions belonging to the series (ROH)sub(n)H + are detected when sampling up to 100-torr alcohol vapor with the molecular beam. No parent cluster molecular ions are detected. Experiments are described which exclude ion-molecule reactions in the mass spectrometer ion source as a possible origin of the cluster ions. Experimental evidence shows that nozzle temperature primarily influences the equilibrium distribution of clusters present in the nozzle source. From the dependences of relative cluster ion intensities on nozzle source temperature, the heats of formation of oligomers of the alcohols are estimated. Cooperative hydrogen bonding is not detected, expect for trifluoroethanol, where the trimer is found to be the most stable cluster. (orig.)

  3. Laser sources and techniques for spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kung, A.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    This program focuses on the development of novel laser and spectroscopic techniques in the IR, UV, and VUV regions for studying combustion related molecular dynamics at the microscopic level. Laser spectroscopic techniques have proven to be extremely powerful in the investigation of molecular processes which require very high sensitivity and selectivity. The authors approach is to use quantum electronic and non-linear optical techniques to extend the spectral coverage and to enhance the optical power of ultrahigh resolution laser sources so as to obtain and analyze photoionization, fluorescence, and photoelectron spectra of jet-cooled free radicals and of reaction products resulting from unimolecular and bimolecular dissociations. New spectroscopic techniques are developed with these sources for the detection of optically thin and often short-lived species. Recent activities center on regenerative amplification of high resolution solid-state lasers, development of tunable high power mid-IR lasers and short-pulse UV/VUV tunable lasers, and development of a multipurpose high-order suppressor crossed molecular beam apparatus for use with synchrotron radiation sources. This program also provides scientific and technical support within the Chemical Sciences Division to the development of LBL`s Combustion Dynamics Initiative.

  4. Optically pumped semiconductor lasers for atomic and molecular physics

    Science.gov (United States)

    Burd, S.; Leibfried, D.; Wilson, A. C.; Wineland, D. J.

    2015-03-01

    Experiments in atomic, molecular and optical (AMO) physics rely on lasers at many different wavelengths and with varying requirements on spectral linewidth, power and intensity stability. Optically pumped semiconductor lasers (OPSLs), when combined with nonlinear frequency conversion, can potentially replace many of the laser systems currently in use. We are developing a source for laser cooling and spectroscopy of Mg+ ions at 280 nm, based on a frequency quadrupled OPSL with the gain chip fabricated at the ORC at Tampere Univ. of Technology, Finland. This OPSL system could serve as a prototype for many other sources used in atomic and molecular physics.

  5. Molecular techniques: An overview of methods for the detection of ...

    African Journals Online (AJOL)

    Several DNA molecular markers are now available for use in surveillance and investigation of food-borne outbreaks that were previously difficult to detect. The results from several sources of literature indicate substantially different degrees of sensitivities between conventional detection methods and molecular-based ...

  6. Compact ion accelerator source

    Science.gov (United States)

    Schenkel, Thomas; Persaud, Arun; Kapadia, Rehan; Javey, Ali

    2014-04-29

    An ion source includes a conductive substrate, the substrate including a plurality of conductive nanostructures with free-standing tips formed on the substrate. A conductive catalytic coating is formed on the nanostructures and substrate for dissociation of a molecular species into an atomic species, the molecular species being brought in contact with the catalytic coating. A target electrode placed apart from the substrate, the target electrode being biased relative to the substrate with a first bias voltage to ionize the atomic species in proximity to the free-standing tips and attract the ionized atomic species from the substrate in the direction of the target electrode.

  7. NGLview-interactive molecular graphics for Jupyter notebooks.

    Science.gov (United States)

    Nguyen, Hai; Case, David A; Rose, Alexander S

    2018-04-01

    NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more. The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics. asr.moin@gmail.com.

  8. Gas chromatography-mass spectrometry with supersonic molecular beams.

    Science.gov (United States)

    Amirav, Aviv; Gordin, Alexander; Poliak, Marina; Fialkov, Alexander B

    2008-02-01

    Gas chromatography-mass spectrometry (GC-MS) with supersonic molecular beams (SMBs) (also named Supersonic GC-MS) is based on GC and MS interface with SMBs and on the electron ionization (EI) of vibrationally cold analytes in the SMBs (cold EI) in a fly-through ion source. This ion source is inherently inert and further characterized by fast response and vacuum background filtration capability. The same ion source offers three modes of ionization including cold EI, classical EI and cluster chemical ionization (CI). Cold EI, as a main mode, provides enhanced molecular ions combined with an effective library sample identification, which is supplemented and complemented by a powerful isotope abundance analysis method and software. The range of low-volatility and thermally labile compounds amenable for analysis is significantly increased owing to the use of the contact-free, fly-through ion source and the ability to lower sample elution temperatures through the use of high column carrier gas flow rates. Effective, fast GC-MS is enabled particularly owing to the possible use of high column flow rates and improved system selectivity in view of the enhancement of the molecular ion. This fast GC-MS with SMB can be further improved via the added selectivity of MS-MS, which by itself benefits from the enhancement of the molecular ion, the most suitable parent ion for MS-MS. Supersonic GC-MS is characterized by low limits of detection (LOD), and its sensitivity is superior to that of standard GC-MS, particularly for samples that are hard for analysis. The GC separation of the Supersonic GC-MS can be improved with pulsed flow modulation (PFM) GC x GC-MS. Electron ionization LC-MS with SMB can also be combined with the Supersonic GC-MS, with fast and easy switching between these two modes of operation. (c) 2008 John Wiley & Sons, Ltd.

  9. SPECTRAL LINE SURVEY TOWARD MOLECULAR CLOUDS IN THE LARGE MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri; Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Center for Computational Sciences, The University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Kawamura, Akiko [National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo, 181-8588 (Japan)

    2016-02-20

    Spectral line survey observations of seven molecular clouds in the Large Magellanic Cloud (LMC) have been conducted in the 3 mm band with the Mopra 22 m telescope to reveal chemical compositions in low metallicity conditions. Spectral lines of fundamental species such as CS, SO, CCH, HCN, HCO{sup +}, and HNC are detected in addition to those of CO and {sup 13}CO, while CH{sub 3}OH is not detected in any source and N{sub 2}H{sup +} is marginally detected in two sources. The molecular-cloud scale (10 pc scale) chemical composition is found to be similar among the seven sources regardless of different star formation activities, and hence, it represents the chemical composition characteristic of the LMC without influences by star formation activities. In comparison with chemical compositions of Galactic sources, the characteristic features are (1) deficient N-bearing molecules, (2) abundant CCH, and (3) deficient CH{sub 3}OH. Feature (1) is due to a lower elemental abundance of nitrogen in the LMC, whereas features (2) and (3) seem to originate from extended photodissociation regions and warmer temperature in cloud peripheries due to a lower abundance of dust grains in the low metallicity condition. In spite of general resemblance of chemical abundances among the seven sources, the CS/HCO{sup +} and SO/HCO{sup +} ratios are found to be slightly higher in a quiescent molecular cloud. An origin of this trend is discussed in relation to possible depletion of sulfur along the molecular cloud formation.

  10. Far-infrared observations of Sagittarius B2 - reconsideration of source structure

    International Nuclear Information System (INIS)

    Thronson, H.A. Jr.; Harper, D.A.; Yerkes Observatory, Williams Bay, WI)

    1986-01-01

    New moderate-angular-resolution far-infrared observations of the Sagittarius B2 star-forming region are presented, discussed, and compared with recent radio molecular and continuum observations of this source. In contrast to previous analyses, its far-infrared spectrum is interpreted as the result of a massive frigid cloud overlying a more-or-less normal infrared source, a natural explanation for the object's previously-noted peculiarities. The characteristics derived for the obscuring cloud are similar to those found for the W51 MAIN object. Both sources have high sub-millimeter surface brightness, a high ratio of sub-millimeter to far-infrared flux, and numerous regions of molecular maser emission. 28 references

  11. Development of a Submillimeter Multipass Spectrometer for the Study of Molecular Ions

    Science.gov (United States)

    Carroll, A.; Rocher, B.; Laas, J. C.; Deprince, B. A.; Hays, B.; Weaver, S. L. Widicus; Lang, S.

    2012-06-01

    We have developed a multipass spectrometer for the submillimeter spectral region that is being used to study molecular ions through gas phase spectroscopy. The optical configuration is based on the design of Perry and coworkers that was implemented in the optical regime. To our knowledge, this is the first implementation of this optical configuration at long wavelengths. The setup involves two nearly concentric spherical mirrors that focus the multiple beam passes into a small area, or ``waist'', in the middle of the sample chamber. A supersonic molecular beam is coupled to the setup so that the molecular beam crosses the optical path at the waist. Initial studies have focused on neutral test molecules to probe the physical properties of the molecular beam under various arrangements of the molecular source relative to the optical path. Current studies focus on coupling a plasma discharge source to the setup to enable the study of molecular ions. Here we present the design of this instrument, compare the spectrometer capabilities to a traditional single pass spectrometer, and discuss the results of initial spectroscopic studies.

  12. A Molecular Description of Cellulose Biosynthesis

    Science.gov (United States)

    McNamara, Joshua T.; Morgan, Jacob L.W.; Zimmer, Jochen

    2016-01-01

    Cellulose is the most abundant biopolymer on Earth, and certain organisms from bacteria to plants and animals synthesize cellulose as an extracellular polymer for various biological functions. Humans have used cellulose for millennia as a material and an energy source, and the advent of a lignocellulosic fuel industry will elevate it to the primary carbon source for the burgeoning renewable energy sector. Despite the biological and societal importance of cellulose, the molecular mechanism by which it is synthesized is now only beginning to emerge. On the basis of recent advances in structural and molecular biology on bacterial cellulose synthases, we review emerging concepts of how the enzymes polymerize glucose molecules, how the nascent polymer is transported across the plasma membrane, and how bacterial cellulose biosynthesis is regulated during biofilm formation. Additionally, we review evolutionary commonalities and differences between cellulose synthases that modulate the nature of the cellulose product formed. PMID:26034894

  13. Development of novel HER2 inhibitors against gastric cancer derived from flavonoid source of Syzygium alternifolium through molecular dynamics and pharmacophore-based screening

    Directory of Open Access Journals (Sweden)

    Babu TMC

    2016-11-01

    Full Text Available Tirumalasetty Muni Chandra Babu,1 Aluru Rammohan,2 Vijaya Bhaskar Baki,1 Savita Devi,3 Duvvuru Gunasekar,2 Wudayagiri Rajendra1 1Bioinformatics Center, Division of Molecular Biology, Department of Zoology, 2Natural Products Division, Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, 3Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India Abstract: Continuous usage of synthetic chemotherapeutic drugs causes adverse effects, which prompted for the development of alternative therapeutics for gastric cancer from natural source. This study was carried out with a specific aim to screen gastroprotective compounds from the fruits of Syzygium alternifolium (Myrtaceae. Three flavonoids, namely, 1 5-hydroxy-7,4'-dimethoxy-6,8-di-C-methylflavone, 2 kaempferol-3-O-β-D-glucopyranoside, and 3 kaempferol-3-O-α-L-rhamnopyranoside were isolated from the above medicinal plant by employing silica gel column chromatography and are characterized by NMR techniques. Antigastric cancer activity of these flavonoids was examined on AGS cell lines followed by cell cycle progression assay. In addition, pharmacophore-based screening and molecular dynamics of protein–ligand complex were carried out to identify potent scaffolds. The results showed that compounds 2 and 3 exhibited significant cytotoxic effect, whereas compound 1 showed moderate effect on AGS cells by inhibiting G2/M phase of cell cycle. Molecular docking analysis revealed that compound 2 has higher binding energies on human growth factor receptor-2 (HER2. The constructed pharmacophore models reveal that the compounds have more number of H-bond Acc/Don features which contribute to the inhibition of HER2 activity. By selecting these features, 34 hits were retrieved using the query compound 2. Molecular dynamic simulations (MDS of protein–ligand complexes demonstrated conspicuous

  14. Molecular beam studies with a time-of-flight machine

    International Nuclear Information System (INIS)

    Beijerinck, H.C.W.

    1975-01-01

    The study concerns the development of the time-of-flight method for the velocity analysis of molecular beams and its application to the measurement of the velocity dependence of the total cross-section of the noble gases. It reviews the elastic scattering theory, both in the framework of classical mechanics and in the quantum mechanical description. Attention is paid to the semiclassical correspondence of classical particle trajectories with the partial waves of the quantum mechanical solution. The total cross-section and the small angle differential cross-section are discussed with special emphasis on their relation. The results of this chapter are used later to derive the correction on the measured total cross-section due to the finite angular resolution of the apparatus. Reviewed also is the available information on the intermolecular potential of the Ar-Ar system. Then a discussion of the measurement of total cross-sections with the molecular beam method and the time-of-flight method is compared to other methods used. It is shown that the single burst time-of-flight method can be developed into a reliable and well-calibrated method for the analysis of the velocity distribution of molecular beams. A comparison of the single burst time-of-flight method with the cross-correlation time-of-flight method shows that the two methods are complementary and that the specific experimental circumstances determine which method is to be preferred. Molecular beam sources are discussed. The peaking factor formalism is introduced and helps to compare the performance of different types of sources. The effusive and the supersonic source are treated and recent experimental results are given. The multichannel source is treated in more detail. For the opaque mode, an experimental investigation of the velocity distribution and the angular distribution of the flow pattern is presented. Comparison of these results with Monte Carlo calculations for free molecular flow in a cylindrical

  15. Molecular biomarkers for sources of organic matter in lacustrine sediments in a subtropical lake in China.

    Science.gov (United States)

    Wang, Yan-Hua; Yang, Hao; Chen, Xia; Zhang, Ji-Xiang; Ou, Jie; Xie, Biao; Huang, Chang-Chun

    2013-05-01

    N-alkanes distributions and stable isotopic compositions (δ(13)C and δ(15)N) in the lacustrine sediments of Shijiu lake were measured to assess whether biological source information was recorded in the molecular biomarker. Results showed regular unimodal n-alkanes distribution in range of C16-C33 with strong predominance of odd-numbered n-alkanes, maximizing at C29. The δ(15)N for SON were uniformly low, ranging from -6.7‰ to 3.8‰ and C/N ratios ranged from 6.6 to 10.0, suggesting that most of organic matter was influenced by terrestrial characteristics of the watershed. The δ(13)C for C27 to C31n-alkanes and for SOC varied from -32.9‰ to -26.6‰ and -23.4‰ to -21.6‰, respectively, falling within the range of corresponding n-alkanes in leaves mainly from C3 land plants. The values of C/N, CPI, OEP, ACL and C27/C31 exhibit similar temporal changes with the primary production, showing enhanced eutrophication resulted from increased anthropogenic activities in Shijiu lake from 1852 to 2010. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  17. The Publicly Available Prebiotic Interstellar Molecular Survey (primos): Expanding Spectroscopic Characterizations, Extending to New Sources, and Adding to the Known Molecular Inventory

    Science.gov (United States)

    McGuire, Brett A.; Carroll, P. Brandon; Corby, Joanna F.; Loomis, Ryan A.; Blake, Geoffrey A.; Hollis, Jan M.; Lovas, Frank J.; Jewell, Philip R.; Remijan, Anthony J.

    2013-06-01

    The publicly available Green Bank Telescope PRebiotic Interstellar MOlecular Survey (PRIMOS) conducted towards Sgr B2(N) provides high resolution, high-sensitivity observations with near-continuous frequency coverage from ˜300 MHz - 50 GHz. Of the eleven new molecular detections in the last year, five (45%) are a direct result of the PRIMOS observations. Further, these observations have recently been used to detect the predicted, but previously unobserved, J = 1-0 and J=2-1 transitions of the newly detected l-C_3H^+ ion. Here, we discuss the analysis of these transitions, as well as recent work to extend the PRIMOS observations to three new regions of interest: VY Canis Majoris, IRC+10216, and NGC 2023. Finally, we highlight the utility of cm-wave surveys in new molecular detections, as well as the value of publicly-available surveys in the approaching era of data-enabled, analysis-limited astrochemistry.

  18. Behaviors of beryllium compensation doping in InGaAsP grown by gas source molecular beam epitaxy

    Science.gov (United States)

    Ma, Y. J.; Zhang, Y. G.; Gu, Y.; Xi, S. P.; Chen, X. Y.; Liang, Baolai; Juang, Bor-Chau; Huffaker, Diana L.; Du, B.; Shao, X. M.; Fang, J. X.

    2017-07-01

    We report structural properties as well as electrical and optical behaviors of beryllium (Be)-doped InGaAsP lattice-matched to InP grown by gas source molecular beam epitaxy. P type layers present a high degree of compensation on the order of 1018 cm-3, and for Be densities below 9.5×1017 cm-3, they are found to be n type. Enhanced incorporation of oxygen during Be doping is observed by secondary ion mass spectroscopy. Be in forms of interstitial donors or donor-like Be-O complexes for cell temperatures below 800°C is proposed to account for such anomalous compensation behaviors. A constant photoluminescence energy of 0.98 eV without any Moss-Burstein shift for Be doping levels up to 1018 cm-3 along with increased emission intensity due to passivation effect of Be is also observed. An increasing number of minority carriers tend to relax via Be defect state-related Shockley-Read-Hall recombination with the increase of Be doping density.

  19. Behaviors of beryllium compensation doping in InGaAsP grown by gas source molecular beam epitaxy

    Directory of Open Access Journals (Sweden)

    Y. J. Ma

    2017-07-01

    Full Text Available We report structural properties as well as electrical and optical behaviors of beryllium (Be-doped InGaAsP lattice-matched to InP grown by gas source molecular beam epitaxy. P type layers present a high degree of compensation on the order of 1018 cm−3, and for Be densities below 9.5×1017 cm−3, they are found to be n type. Enhanced incorporation of oxygen during Be doping is observed by secondary ion mass spectroscopy. Be in forms of interstitial donors or donor-like Be-O complexes for cell temperatures below 800°C is proposed to account for such anomalous compensation behaviors. A constant photoluminescence energy of 0.98 eV without any Moss-Burstein shift for Be doping levels up to 1018 cm−3 along with increased emission intensity due to passivation effect of Be is also observed. An increasing number of minority carriers tend to relax via Be defect state-related Shockley-Read-Hall recombination with the increase of Be doping density.

  20. Advanced spallation neutron sources for condensed matter research

    International Nuclear Information System (INIS)

    Lovesey, S.W.; Stirling, G.C.

    1984-03-01

    Advanced spallation neutron sources afford significant advantages over existing high flux reactors. The effective flux is much greater than that currently available with reactor sources. A ten-fold increase in neutron flux will be a major benefit to a wide range of condensed matter studies, and it will realise important experiments that are marginal at reactor sources. Moreover, the high intensity of epithermal neutrons open new vistas in studies of electronic states and molecular vibrations. (author)

  1. A combined thermal dissociation and electron impact ionization source for radioactive ion beam generation (abstract)a

    International Nuclear Information System (INIS)

    Alton, G.D.; Williams, C.

    1996-01-01

    The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. copyright 1996 American Institute of Physics

  2. In-source collision induced dissociation of inorganic explosives for mass spectrometric signature detection and chemical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Forbes, Thomas P., E-mail: thomas.forbes@nist.gov; Sisco, Edward

    2015-09-10

    The trace detection, bulk quantification, and chemical imaging of inorganic explosives and components was demonstrated utilizing in-source collision induced dissociation (CID) coupled with laser desorption/ionization mass spectrometry (LDI-MS). The incorporation of in-source CID provided direct control over the extent of adduct and cluster fragmentation as well as organic noise reduction for the enhanced detection of both the elemental and molecular ion signatures of fuel-oxidizer mixtures and other inorganic components of explosive devices. Investigation of oxidizer molecular anions, specifically, nitrates, chlorates, and perchlorates, identified that the optimal in-source CID existed at the transition between fragmentation of the ionic salt bonds and molecular anion bonds. The chemical imaging of oxidizer particles from latent fingerprints was demonstrated, including both cation and anion components in positive and negative mode mass spectrometry, respectively. This investigation demonstrated LDI-MS with in-source CID as a versatile tool for security fields, as well as environmental monitoring and nuclear safeguards, facilitating the detection of elemental and molecular inorganic compounds at nanogram levels. - Highlights: • In-source CID enhanced detection of elemental inorganics up to 1000-fold. • In-source CID optimization of polyatomic oxidizers enhanced detection up to 100-fold. • Optimal CID identified at transition from breaking ionic salt to molecular anion bonds. • Trace detection of inorganic explosives at nanogram levels was demonstrated. • Oxidizer particles were chemically imaged directly from latent fingerprints.

  3. A new concept Tandem thermal dissociator/electron impact ion source for RIB generation

    International Nuclear Information System (INIS)

    Alton, G.D.; Williams, C.

    1995-01-01

    An innovative thermal dissociation/electron impact ionization positive ion source is presently under design at the Oak Ridge National Laboratory for potential use for generating RIBs at the Holifield Radioactive Ion Beam Facility (HRIBF). Because of the low probability of simultaneously dissociating and efficiently ionizing the individual atomic constituents with conventional, hot-cathode, electron-impact ion sources, the ion beams extracted from these sources often appear as a mixture of several molecular sideband beams. In this way, the intensity of the species of interest is diluted. We have conceived an Ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high efficiency characteristics of an electron impact ionization source. If the concept proves to be a viable option, the source will be used as a complement to the electron beam plasma ion sources already in use at the HRIBF. The design features and principles of operation of the source are described in this article

  4. A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

    Science.gov (United States)

    Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

    1993-01-01

    We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

  5. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

    Science.gov (United States)

    Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R; Smith, Jeremy C; Kasson, Peter M; van der Spoel, David; Hess, Berk; Lindahl, Erik

    2013-04-01

    Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. GROMACS is an open source and free software available from http://www.gromacs.org. Supplementary data are available at Bioinformatics online.

  6. Self-assembled GaInNAs/GaAsN quantum dot lasers: solid source molecular beam epitaxy growth and high-temperature operation

    Directory of Open Access Journals (Sweden)

    Yoon SF

    2006-01-01

    Full Text Available AbstractSelf-assembled GaInNAs quantum dots (QDs were grown on GaAs (001 substrate using solid-source molecular-beam epitaxy (SSMBE equipped with a radio-frequency nitrogen plasma source. The GaInNAs QD growth characteristics were extensively investigated using atomic-force microscopy (AFM, photoluminescence (PL, and transmission electron microscopy (TEM measurements. Self-assembled GaInNAs/GaAsN single layer QD lasers grown using SSMBE have been fabricated and characterized. The laser worked under continuous wave (CW operation at room temperature (RT with emission wavelength of 1175.86 nm. Temperature-dependent measurements have been carried out on the GaInNAs QD lasers. The lowest obtained threshold current density in this work is ∼1.05 kA/cm2from a GaInNAs QD laser (50 × 1,700 µm2 at 10 °C. High-temperature operation up to 65 °C was demonstrated from an unbonded GaInNAs QD laser (50 × 1,060 µm2, with high characteristic temperature of 79.4 K in the temperature range of 10–60 °C.

  7. Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications

    International Nuclear Information System (INIS)

    Schiesser, Alexander; Schaefer, Rolf

    2009-01-01

    This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10 11 molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

  8. CaI and SrI molecules for iodine determination by high-resolution continuum source graphite furnace molecular absorption spectrometry: Greener molecules for practical application.

    Science.gov (United States)

    Zanatta, Melina Borges Teixeira; Nakadi, Flávio Venâncio; da Veiga, Márcia Andreia Mesquita Silva

    2018-03-01

    A new method to determine iodine in drug samples by high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) has been developed. The method measures the molecular absorption of a diatomic molecule, CaI or SrI (less toxic molecule-forming reagents), at 638.904 or 677.692nm, respectively, and uses a mixture containing 5μg of Pd and 0.5μg of Mg as chemical modifier. The method employs pyrolysis temperatures of 1000 and 800°C and vaporization temperatures of 2300 and 2400°C for CaI and SrI, respectively. The optimized amounts of Ca and Sr as molecule-forming reagents are 100 and 150µg, respectively. On the basis of interference studies, even small chlorine concentrations reduce CaI and SrI absorbance significantly. The developed method was used to analyze different commercial drug samples, namely thyroid hormone pills with three different iodine amounts (15.88, 31.77, and 47.66µg) and one liquid drug with 1% m v -1 active iodine in their compositions. The results agreed with the values informed by the manufacturers (95% confidence level) regardless of whether CaI or SrI was determined. Therefore, the developed method is useful for iodine determination on the basis of CaI or SrI molecular absorption. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Uncertainty estimates for theoretical atomic and molecular data

    International Nuclear Information System (INIS)

    Chung, H-K; Braams, B J; Bartschat, K; Császár, A G; Drake, G W F; Kirchner, T; Kokoouline, V; Tennyson, J

    2016-01-01

    Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structures and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering. (topical review)

  10. High-temperature operation of self-assembled GaInNAs/GaAsN quantum-dot lasers grown by solid-source molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Liu, C.Y.; Yoon, S.F.; Sun, Z.Z.; Yew, K.C.

    2006-01-01

    Self-assembled GaInNAs/GaAsN single layer quantum-dot (QD) lasers grown using solid-source molecular-beam epitaxy have been fabricated and characterized. Temperature-dependent measurements have been carried out on the GaInNAs QD lasers. The lowest obtained threshold current density in this work is ∼1.05 kA/cm 2 from a GaInNAs QD laser (50x1700 μm 2 ) at 10 deg. C. High-temperature operation up to 65 deg. C was also demonstrated from an unbonded GaInNAs QD laser (50x1060 μm 2 ), with high characteristic temperature of 79.4 K in the temperature range of 10-60 deg. C

  11. Metabolomics Workbench (MetWB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego,...

  12. Pulsed, atmospheric pressure plasma source for emission spectrometry

    Science.gov (United States)

    Duan, Yixiang; Jin, Zhe; Su, Yongxuan

    2004-05-11

    A low-power, plasma source-based, portable molecular light emission generator/detector employing an atmospheric pressure pulsed-plasma for molecular fragmentation and excitation is described. The average power required for the operation of the plasma is between 0.02 W and 5 W. The features of the optical emission spectra obtained with the pulsed plasma source are significantly different from those obtained with direct current (dc) discharge higher power; for example, strong CH emission at 431.2 nm which is only weakly observed with dc plasma sources was observed, and the intense CN emission observed at 383-388 nm using dc plasma sources was weak in most cases. Strong CN emission was only observed using the present apparatus when compounds containing nitrogen, such as aniline were employed as samples. The present apparatus detects dimethylsulfoxide at 200 ppb using helium as the plasma gas by observing the emission band of the CH radical. When coupled with a gas chromatograph for separating components present in a sample to be analyzed, the present invention provides an apparatus for detecting the arrival of a particular component in the sample at the end of the chromatographic column and the identity thereof.

  13. Molecular-beam spectroscopy of interhalogen molecules

    International Nuclear Information System (INIS)

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of 79 Br 35 Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed

  14. Physics with fast molecular-ion beams

    International Nuclear Information System (INIS)

    Kanter, E.P.

    1980-01-01

    Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented

  15. Molecular Entropy, Thermal Efficiency, and Designing of Working Fluids for Organic Rankine Cycles

    Science.gov (United States)

    Wang, Jingtao; Zhang, Jin; Chen, Zhiyou

    2012-06-01

    A shortage of fossil energy sources boosts the utilization of renewable energy. Among numerous novel techniques, recovering energy from low-grade heat sources through power generation via organic Rankine cycles (ORCs) is one of the focuses. Properties of working fluids are crucial for the ORC's performance. Many studies have been done to select proper working fluids or to design new working fluids. However, no researcher has systematically investigated the relationship between molecular structures and thermal efficiencies of various working fluids for an ideal ORC. This paper has investigated the interrelations of molecular structures, molecular entropies, and thermal efficiencies of various working fluids for an ideal ORC. By calculating thermal efficiencies and molecular entropies, we find that the molecular entropy is the most appropriate thermophysical property of a working fluid to determine how much energy can be converted into work and how much cannot in a system. Generally speaking, working fluids with low entropies will generally have high thermal efficiency for an ideal ORC. Based on this understanding, the direct interrelations of molecular structures and entropies provide an explicit interrelation between molecular structures and thermal efficiencies, and thus provide an insightful direction for molecular design of novel working fluids for ORCs.

  16. A combination thermal dissociation/electron impact ionization source for RIB generation

    International Nuclear Information System (INIS)

    Alton, G.D.; Cui, B.; Welton, R.F.

    1996-01-01

    The flourishing interest in radioactive ion beams (RIBs) with intensities adequate for astrophysics and nuclear physics research place a premium on targets that will swiftly release trace amounts of short lived radio-nuclei in the presence of bulk quantities of target material and ion sources that have the capability of efficiently ionizing the release products. Because of the low probability of simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecules containing the element of interest with conventional, hot-cathode, electron-impact ion sources, the species of interest is often distributed in several mass channels in the form of molecular sideband beams and, consequently, the intensity is diluted. The authors have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high efficiency characteristics of an electron impact ionization source to address these problems. If the concept proves to be a viable option, the source will be used as a complement to the electron beam plasma ion sources already in use at the HRIBF. The design features and principles of operation of the source are described in this article

  17. Shocked molecular hydrogen in the supernova remnant IC 443

    International Nuclear Information System (INIS)

    Burton, M.G.; Brand, P.W.J.L.; Webster, A.S.

    1988-01-01

    Emission from the υ = 1-0 S(1) line of molecular hydrogen has been mapped over a section of the supernova remnant IC 443. The emission originates in a sinuous ridge where the expanding shell of the SNR is interacting with a molecular cloud. The relative intensities of the 1-0 S(1), 1-0 S(0) and 2-1 S(1) lines at 2.1-2.2 μm were measured and found to be characteristic of shock-excitation of the gas. The ridge shows bright spots which are possibly density enhancements in the molecular cloud. The total luminosity of the molecular hydrogen lines in the mapped region is estimated to be about 1000 times the solar luminosity, making IC 443 one of the most luminous galactic molecular hydrogen sources yet detected. (author)

  18. On simulation of local fluxes in molecular junctions

    Science.gov (United States)

    Cabra, Gabriel; Jensen, Anders; Galperin, Michael

    2018-05-01

    We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

  19. Humidity Effects on Fragmentation in Plasma-Based Ambient Ionization Sources.

    Science.gov (United States)

    Newsome, G Asher; Ackerman, Luke K; Johnson, Kevin J

    2016-01-01

    Post-plasma ambient desorption/ionization (ADI) sources are fundamentally dependent on surrounding water vapor to produce protonated analyte ions. There are two reports of humidity effects on ADI spectra. However, it is unclear whether humidity will affect all ADI sources and analytes, and by what mechanism humidity affects spectra. Flowing atmospheric pressure afterglow (FAPA) ionization and direct analysis in real time (DART) mass spectra of various surface-deposited and gas-phase analytes were acquired at ambient temperature and pressure across a range of observed humidity values. A controlled humidity enclosure around the ion source and mass spectrometer inlet was used to create programmed humidity and temperatures. The relative abundance and fragmentation of molecular adduct ions for several compounds consistently varied with changing ambient humidity and also were controlled with the humidity enclosure. For several compounds, increasing humidity decreased protonated molecule and other molecular adduct ion fragmentation in both FAPA and DART spectra. For others, humidity increased fragment ion ratios. The effects of humidity on molecular adduct ion fragmentation were caused by changes in the relative abundances of different reagent protonated water clusters and, thus, a change in the average difference in proton affinity between an analyte and the population of water clusters. Control of humidity in ambient post-plasma ion sources is needed to create spectral stability and reproducibility.

  20. Microporous and meso porous molecular sieves

    International Nuclear Information System (INIS)

    Araujo, Antonio Souza de

    1999-01-01

    In this work, general aspects on the microporous and mesoporous molecular sieves using inorganic sources of aluminium, silicon, phosphorous, water and structural organic templates are reviewed. The nomenclature, synthesis, structure, acidity and chemical functionality of microporous zeolites and silico alumino phosphate, besides mesoporous MCM-41 material, will be emphasized. (author)

  1. Molecular biogeochemical provinces in the Atlantic Surface Ocean

    Science.gov (United States)

    Koch, B. P.; Flerus, R.; Schmitt-Kopplin, P.; Lechtenfeld, O. J.; Bracher, A.; Cooper, W.; Frka, S.; Gašparović, B.; Gonsior, M.; Hertkorn, N.; Jaffe, R.; Jenkins, A.; Kuss, J.; Lara, R. J.; Lucio, M.; McCallister, S. L.; Neogi, S. B.; Pohl, C.; Roettgers, R.; Rohardt, G.; Schmitt, B. B.; Stuart, A.; Theis, A.; Ying, W.; Witt, M.; Xie, Z.; Yamashita, Y.; Zhang, L.; Zhu, Z. Y.; Kattner, G.

    2010-12-01

    One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, which was performed on a cruise with RV Polarstern, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) on a North-South transect in the Atlantic surface ocean in order to relate the data to different biological, climatic, oceanographic, and meteorological regimes as well as to terrestrial input from riverine and atmospheric sources. Our goal was to achieve a high resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied ultrahigh resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS), nutrient, trace element, amino acid, and lipid analyses and other biogeochemical measurements for 220 samples from the upper water column (0-200m) and eight deep profiles. Various spectroscopic techniques were applied continuously in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessing DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work and pCO2 concentrations. Combining molecular organic techniques and inductively coupled plasma mass spectrometry (ICP-MS) established an important link between organic and inorganic biogeochemical studies. Multivariate statistics, primarily based on FT-ICR-MS data for 220 samples, allowed identifying geographical clusters which matched ecological provinces proposed previously by Longhurst (2007). Our study demonstrated that marine DOM carries molecular information reflecting the “history” of ocean water masses. This information can be used to define molecular biogeochemical provinces and to improve our understanding of element fluxes in

  2. Molecular beam epitaxy for the future

    International Nuclear Information System (INIS)

    Takahashi, K.

    1984-01-01

    Molecular beam epitaxy (MBE) is most commonly used to fabricate super-lattices, high electron mobility transistors, multi-quantum well lasers and other new semiconductor devices by utilizing its excellent controlability. MBE for the future is presumed to include techniques such as metalorganic chemical vapor deposition, photochemical reaction process using gas sources and ion implantation. A report on the crystal growth of GaAs using metalorganics, trimethylgallium and triethylgallium, which are usually used in chemical vapor deposition, as gaseous sources of gallium in an MBE system is made. (Author) [pt

  3. Synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    van Steenbergen, A.

    1979-01-01

    As a result of the exponential growth of the utilization of synchrotron radiation for research in the domain of the material sciences, atomic and molecular physics, biology and technology, a major construction activity has been generated towards new dedicated electron storage rings, designed optimally for synchrotron radiation applications, also, expansion programs are underway at the existing facilities, such as DORIS, SPEAR, and VEPP. In this report the basic properties of synchrotron radiation will be discussed, a short overview will be given of the existing and new facilities, some aspects of the optimization of a structure for a synchrotron radiation source will be discussed and the addition of wigglers and undulators for spectrum enhancement will be described. Finally, some parameters of an optimized synchrotron radiation source will be given.

  4. Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking

    Science.gov (United States)

    Fong, T.-T.; Griffin, Dale W.; Lipp, E.K.

    2005-01-01

    Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-?? concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

  5. Optical Pumping of Molecular Gases

    Science.gov (United States)

    1976-04-01

    ser emission ott a The typical experimental apparatus is shown i.- Fig. *series of green and yellow molecular B-X’-basnd transi- 2. For B-bantd optical...with A, at 0. 473 pim and that Na2 may operate as a flash -lamp -pumped laser X,... at 0. 54 umn the Doppler widths are AwD - 12.42 source with buffer

  6. 1978 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  7. 1979 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  8. 1980 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1982-02-01

    This annotated bibliography lists 2866 works on atomic and molecular processes reported in publications dated 1980. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  9. Molecular confirmation of shampoo as the putative source of Pseudomonas aeruginosa-induced postgrooming furunculosis in a dog.

    Science.gov (United States)

    Tham, Heng L; Jacob, Megan E; Bizikova, Petra

    2016-08-01

    An acute onset furunculosis due to Pseudomonas aeruginosa following grooming is a well recognized entity. Although contaminated shampoos have been suspected to be the source of the infection, a molecular confirmation of this association has been missing. This case report describes a dog with postgrooming furunculosis in which Pseudomonas aeruginosa with an identical genetic fingerprint was isolated from the skin lesions as well as from the shampoo used prior to the disease onset. The dog presented for lethargy, anorexia, pain and rapidly progressing skin lesions consistent with haemorrhagic papules, pustules, coalescing ulcers and crusts localized to the dorsal and lateral aspects of the thorax and gluteal region, which developed within 24 h after a bath. Cytology demonstrated suppurative inflammation with occasional intracellular rod-shaped bacteria. Bacterial culture from skin lesions and the shampoo bottle yielded Pseudomonas aeruginosa with an identical pulsed-field gel electrophoresis pattern. Treatment with oral ciprofloxacin and topical antimicrobial shampoo resulted in a complete resolution of skin lesions within eight weeks. Our clinical investigation suggests a link between Pseudomonas-contaminated shampoo and development of postgrooming furunculosis, and underscores the need for hygienic management of shampoos to help limit this disease. © 2016 ESVD and ACVD.

  10. Environmental research at the Advanced Photon Source

    International Nuclear Information System (INIS)

    Kemner, K.M.; Boyanov, M.I.; Eng, P.; Fenter, P.; Heald, S.; Lai, B.; Lee, S.S.; Scheckel, K.G.; Skanthakumar, S.; Sutton, S.R.; Wilson, R.E.

    2010-01-01

    Because of the importance of probing molecular-scale chemical and physical structure of environmental samples in their natural and often hydrated state, synchrotron radiation has been a powerful tool for environmental scientists for decades. Thus, the crucial role that a highly coherent and high-brightness hard X-ray source such as the Advance Photon Source (APS) can play in addressing many of the outstanding questions in molecular environmental science (MES) was recognized even before 'first light' at the facility. No single synchrotron-based technique or experimental approach can adequately address the tremendous temporal and spatial heterogeneities of the chemistry, physics, and biology of natural environmental samples. Thus, it is common at the APS that multiple X-ray techniques and experimental systems are employed to investigate environmental samples, often chosen for their ability to focus on solute species, plants, microbes, organics, interfacial species, or solids.

  11. Photon statistics characterization of a single-photon source

    International Nuclear Information System (INIS)

    Alleaume, R; Treussart, F; Courty, J-M; Roch, J-F

    2004-01-01

    In a recent experiment, we reported the time-domain intensity noise measurement of a single-photon source relying on single-molecule fluorescence control. In this paper, we present data processing starting from photocount timestamps. The theoretical analytical expression of the time-dependent Mandel parameter Q(T) of an intermittent single-photon source is derived from ON↔OFF dynamics. Finally, source intensity noise analysis, using the Mandel parameter, is quantitatively compared with the usual approach relying on the time autocorrelation function, both methods yielding the same molecular dynamical parameters

  12. Music publishing

    OpenAIRE

    Simões, Alberto; Almeida, J. J.

    2003-01-01

    Current music publishing in the Internet is mainly concerned with sound publishing. We claim that music publishing is not only to make sound available but also to define relations between a set of music objects like music scores, guitar chords, lyrics and their meta-data. We want an easy way to publish music in the Internet, to make high quality paper booklets and even to create Audio CD's. In this document we present a workbench for music publishing based on open formats, using open-source t...

  13. Determination of sulfur in human hair using high resolution continuum source graphite furnace molecular absorption spectrometry and its correlation with total protein and albumin

    Science.gov (United States)

    Ozbek, Nil; Baysal, Asli

    2017-04-01

    Human hair is a valuable contributor for biological monitoring. It is an information storage point to assess the effects of environmental, nutritional or occupational sources on the body. Human proteins, amino acids or other compounds are among the key components to find the sources of different effects or disorders in the human body. Sulfur is a significant one of these compounds, and it has great affinity to some metals and compounds. This property of the sulfur affects the human health positively or negatively. In this manuscript, sulfur was determined in hair samples of autistic and age-match control group children via molecular absorption of CS using a high-resolution continuum source graphite furnace atomic absorption spectrometer. For this purpose, hair samples were appropriately washed and dried at 75 °C. Then samples were dissolved in microwave digestion using HNO3 for sulfur determination. Extraction was performed with HCl hydrolysation by incubation for 24 h at 110 °C for total protein and albumin determination. The validity of the method for the sulfur determination was tested using hair standard reference materials. The results were in the uncertainty limits of the certified values at 95% confidence level. Finally correlation of sulfur levels of autistic children's hair with their total protein and albumin levels were done.

  14. Study of the molecular and ionized gas in a possible precursor of an ultra-compact H II region

    Science.gov (United States)

    Ortega, M. E.; Paron, S.; Giacani, E.; Celis Peña, M.; Rubio, M.; Petriella, A.

    2017-10-01

    Aims: We aim to study the molecular and the ionized gas in a possible precursor of an ultra-compact H II region to contribute to the understanding of how high-mass stars build-up their masses once they have reached the zero-age main sequence. Methods: We carried out molecular observations toward the position of the Red MSX source G052.9221-00.4892, using the Atacama Submillimeter Telescope Experiment (ASTE; Chile) in the 12CO J = 3-2, 13CO J = 3-2, C18O J = 3-2, and HCO+J = 4-3 lines with an angular resolution of about 22''. We also present radio continuum observations at 6 GHz carried out with the Jansky Very Large Array (JVLA; USA) interferometer with a synthesized beam of 4.8 arcsec × 4.1 arcsec. The molecular data were used to study the distribution and kinematics of the molecular gas, while the radio continuum data were used to characterize the ionized gas in the region. Combining these observations with public infrared data allowed us to inquire about the nature of the source. Results: The analysis of the molecular observations reveals the presence of a kinetic temperature and H2 column density gradients across the molecular clump in which the Red MSX source G052.9221-00.4892 is embedded, with the hotter and less dense gas in the inner region. The 12CO J = 3-2 emission shows evidence of misaligned massive molecular outflows, with the blue lobe in positional coincidence with a jet-like feature seen at 8 μm. The radio continuum emission shows a slightly elongated compact radio source, with a flux density of about 0.9 mJy, in positional coincidence with the Red MSX source. The polar-like morphology of this compact radio source perfectly matches the hourglass-like morphology exhibited by the source in the Ks band. Moreover, the axes of symmetry of the radio source and the near-infrared nebula are perfectly aligned. Thus, based on the presence of molecular outflows, the slightly elongated morphology of the compact radio source matching the hourglass

  15. ePMV embeds molecular modeling into professional animation software environments.

    Science.gov (United States)

    Johnson, Graham T; Autin, Ludovic; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

    2011-03-09

    Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Gerald: a general environment for radiation analysis and design

    International Nuclear Information System (INIS)

    Boyle, Ch.; Oliveira, P.I.E. de; Oliveira, C.R.E. de; Adams, M.L.; Galan, J.M.

    2005-01-01

    Full text of publication follows: This paper describes the status of the GERALD interactive workbench for the analysis of radiation transport problems. GERALD basically guides the user through the various steps that are necessary to solve a radiation transport problem, and is aimed at education, research and industry. The advantages of such workbench are many: quality assurance of problem setup, interaction of the user with problem solution, preservation of theory and legacy research codes, and rapid proto-typing and testing of new methods. The environment is of general applicability catering for analytical, deterministic and stochastic analysis of the radiation problem and is not tied to one specific solution method or code. However, GERALD is being developed as a portable, modular, open source framework which renders itself quite naturally to the coupling of existing computational tools through specifically developed plug-ins. By offering a common route for setting up, solving and analyzing radiation transport problems GERALD offers the possibility of methods intercomparison and validation. Such flexible radiation transport environment will also facilitate the coupling of radiation physics methods to other physical phenomena and their application to other areas of application such as medical physics and the environment. (authors)

  17. Design of Molecular Materials: Supramolecular Engineering

    Science.gov (United States)

    Simon, Jacques; Bassoul, Pierre

    2001-02-01

    This timely and fascinating book is destined to be recognised as THE book on supramolecular engineering protocols. It covers this sometimes difficult subject in an approachable form, gathering together information from many sources. Supramolecular chemistry, which links organic chemistry to materials science, is one of the fastest growth areas of chemistry research. This book creates a correlation between the structure of single molecules and the physical and chemical properties of the resulting materials. By making systematic changes to the component molecules, the resulting solid can be engineered for optimum performance. There is a clearly written development from synthesis of designer molecules to properties of solids and further on to devices and complex materials systems, providing guidelines for mastering the organisation of these systems. Topics covered include: Systemic chemistry Molecular assemblies Notions of symmetry Supramolecular engineering Principe de Curie Organisation in molecular media Molecular semiconductors Industrial applications of molecular materials This superb book will be invaluable to researchers in the field of supramolecular materials and also to students and teachers of the subject.

  18. Numerical simulation of induction heating thick-walled tubes

    Directory of Open Access Journals (Sweden)

    Lenhard Richard

    2018-01-01

    Full Text Available In the paper is shown the connection of two toolboxes in an Ansys Workbench solution for induction heating. In Ansys Workbench, Maxwell electromagnetism programs and Fluent have been linked. In Maxwell, a simulation of electromagnetic induction was performed, where data on the magnetic field distribution in the heated material was obtained and then transformed into the Fluent program in which the induction heating simulation was performed.

  19. Salmonella source attribution based on microbial subtyping

    DEFF Research Database (Denmark)

    Barco, Lisa; Barrucci, Federica; Olsen, John Elmerdahl

    2013-01-01

    Source attribution of cases of food-borne disease represents a valuable tool for identifying and prioritizing effective food-safety interventions. Microbial subtyping is one of the most common methods to infer potential sources of human food-borne infections. So far, Salmonella microbial subtyping...... source attribution through microbial subtyping approach. It summarizes the available microbial subtyping attribution models and discusses the use of conventional phenotypic typing methods, as well as of the most commonly applied molecular typing methods in the European Union (EU) laboratories...

  20. Optimization of Uranium Molecular Deposition for Alpha-Counting Sources

    Energy Technology Data Exchange (ETDEWEB)

    Monzo, Ellen [Univ. of Minnesota, Duluth, MN (United States); Parsons-Moss, Tashi [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Genetti, Victoria [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Knight, Kimberly [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-12-12

    Method development for molecular deposition of uranium onto aluminum 1100 plates was conducted with custom plating cells at Lawrence Livermore National Laboratory. The method development focused primarily on variation of electrode type, which was expected to directly influence plated sample homogeneity. Solid disc platinum and mesh platinum anodes were compared and data revealed that solid disc platinum anodes produced more homogenous uranium oxide films. However, the activity distribution also depended on the orientation of the platinum electrode relative to the aluminum cathode, starting current, and material composition of the plating cell. Experiments demonstrated these variables were difficult to control under the conditions available. Variation of plating parameters among a series of ten deposited plates yielded variations up to 30% in deposition efficiency. Teflon particles were observed on samples plated in Teflon cells, which poses a problem for alpha activity measurements of the plates. Preliminary electropolishing and chemical polishing studies were also conducted on the aluminum 1100 cathode plates.

  1. Discovery of a point-like very-high-energy gamma-ray source in Monoceros

    International Nuclear Information System (INIS)

    Aharonian, F.A.; Benbow, W.; Berge, D.; Bernlohr, K.; Bolz, O.; Braun, I.; Buhler, R.; Carrigan, S.; Costamante, L.; Domainko, W.; Egberts, K.; Forster, A.; Funk, S.; Hauser, D.; Hermann, G.; Hinton, J.A.; Hofmann, W.; Hoppe, S.; Khelifi, B.; Kosack, K.; Masterson, C.; Panter, M.; Rowell, G.; van Eldik, C.; Volk, H.J.; Akhperjanian, A.G.; Sahakian, V.; Bazer-Bachi, A.R.; Borrel, V.; Marcowith, A.; Olive, J.P.; Beilicke, M.; Cornils, R.; Heinzelmann, G.; Raue, M.; Ripken, J.; Bernlohr, K.; Funk, Seb.; Fussling, M.; Kerschhaggl, M.; Lohse, T.; Schlenker, S.; Schwanke, U.; Boisson, C.; Martin, J.M.; Sol, H.; Brion, E.; Glicenstein, J.F.; Goret, P.; Moulin, E.; Rolland, L.

    2007-01-01

    Aims. The complex Monoceros Loop SNR/Rosette Nebula region contains several potential sources of very-high-energy (VHE) γ-ray emission and two as yet unidentified high-energy EGRET sources. Sensitive VHE observations are required to probe acceleration processes in this region. Methods. The HESS telescope array has been used to search for very high-energy gamma-ray sources in this region. CO data from the NANTEN telescope were used to map the molecular clouds in the region, which could act as target material for γ-ray production via hadronic interactions. Results. We announce the discovery of a new γ-ray source, HESS J0632+057, located close to the rim of the Monoceros SNR. This source is unresolved by HESS and has no clear counterpart at other wavelengths but is possibly associated with the weak X-ray source 1RXS J063258.3+054857, the Be-star MWC148 and/or the lower energy γ-ray source 3EGJ0634+0521. No evidence for an associated molecular cloud was found in the CO data. (authors)

  2. Molecular Rift: Virtual Reality for Drug Designers.

    Science.gov (United States)

    Norrby, Magnus; Grebner, Christoph; Eriksson, Joakim; Boström, Jonas

    2015-11-23

    Recent advances in interaction design have created new ways to use computers. One example is the ability to create enhanced 3D environments that simulate physical presence in the real world--a virtual reality. This is relevant to drug discovery since molecular models are frequently used to obtain deeper understandings of, say, ligand-protein complexes. We have developed a tool (Molecular Rift), which creates a virtual reality environment steered with hand movements. Oculus Rift, a head-mounted display, is used to create the virtual settings. The program is controlled by gesture-recognition, using the gaming sensor MS Kinect v2, eliminating the need for standard input devices. The Open Babel toolkit was integrated to provide access to powerful cheminformatics functions. Molecular Rift was developed with a focus on usability, including iterative test-group evaluations. We conclude with reflections on virtual reality's future capabilities in chemistry and education. Molecular Rift is open source and can be downloaded from GitHub.

  3. Initial vibrational and rotational yields from subexcitation electrons in molecular hydrogen

    International Nuclear Information System (INIS)

    Douthat, D.A.

    1987-01-01

    As the energy of a single source electron injected into a molecular gas is degraded through collisions, initial products include secondary electrons, ions, and excited molecules. Electrons with kinetic energies less than the minimum required for excitation of the lowest electronic state are given the designation subexcitation electrons. These electrons are still capable of exciting vibrational and rotational states of molecular gases. In this calculation, the initial numbers of vibrational and rotational excitations (yields) produced as the subexcitation electrons undergo further energy degradation are determined for molecular hydrogen. The calculation requires a complete set of cross section data for numerical solution of the Boltzmann equation. The initial energy distribution of electrons is taken to be the subexcitation distribution which was determined previously. The initial yields are tabulated for gas temperatures from 50 K to 1500 K for a source electron with initial energy 10 keV. 26 references

  4. Photon acceleration-based radiation sources

    International Nuclear Information System (INIS)

    Hoffman, J. R.; Muggli, P.; Katsouleas, T.; Mori, W. B.; Joshi, C.

    1999-01-01

    The acceleration and deceleration of photons in a plasma provides the means for a series of new radiation sources. Previous work on a DC to AC Radiation Converter (DARC source) has shown variable acceleration of photons having zero frequency (i.e., an electrostatic field) to between 6 and 100 GHz (1-3). These sources all had poor guiding characteristics resulting in poor power coupling from the source to the load. Continuing research has identified a novel way to integrate the DARC source into a waveguide. The so called ''pin structure'' uses stainless steel pins inserted through the narrow side of an X band waveguide to form the electrostatic field pattern (k≠0, ω=0). The pins are spaced such that the absorption band resulting from this additional periodic structure is outside of the X band range (8-12 GHz), in which the normal waveguide characteristics are left unchanged. The power of this X band source is predicted theoretically to scale quadratically with the pin bias voltage as -800 W/(kV) 2 and have a pulse width of -1 ns. Cold tests and experimental results are presented. Applications for a high power, short pulse radiation source extends to the areas of landmine detection, improved radar resolution, and experimental investigations of molecular systems

  5. Implications of recent research on microstructure modifications, through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, metabolic characteristics and nutrition in cool-climate cereal grains and other types of seeds with advanced molecular techniques.

    Science.gov (United States)

    Ying, Yuguang; Zhang, Huihua; Yu, Peiqiang

    2018-02-16

    The cutting-edge synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy have recently been developed. These novel techniques are able to reveal structure features at cellular and molecular levels with the tested tissues being intact. However, to date, the advanced techniques are unfamiliar or unknown to food and feed scientists and have not been used to study the molecular structure changes in cool-climate cereal grain seeds and other types of bio-oil and bioenergy seeds. This article aims to provide some recent research in cool-climate cereal grains and other types of seeds on molecular structures and metabolic characteristics of carbohydrate and protein, and implication of microstructure modification through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, and nutrition with advanced molecular techniques- synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy in the areas of (1) Inherent microstructure of cereal grain seeds; (2) The nutritional values of cereal grains; (3) Impact and modification of heat-related processing to cereal grain; (4) Conventional nutrition evaluation methodology; (5) Synchrotron radiation-based and globar-sourced vibrational (micro)-spectroscopy for molecular structure study and molecular thermal stability and mobility, and (6) Recent molecular spectroscopic technique applications in research on raw, traits altered and processed cool-climate cereal grains and other types of seeds. The information described in this article gives better insights of research progress and update in cool-climate cereal grains and other seeds with advanced molecular techniques.

  6. 1982 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  7. Bibliography of atomic and molecular processes, 1983

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  8. 1985 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  9. 1985 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  10. Bibliography of atomic and molecular processes, 1983

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  11. 1984 Bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1985-04-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  12. 1982 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  13. Progress in ISOL target-ion source systems

    Energy Technology Data Exchange (ETDEWEB)

    Koester, U. [Institut Laue Langevin, 6 Rue Jules Horowitz, F-38042 Grenoble Cedex 9 (France); ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland)], E-mail: koester@ill.fr; Arndt, O. [HGF VISTARS and Institut fuer Kernchemie, Johannes-Gutenberg Universitaet Mainz, D-55128 Mainz (Germany); Bouquerel, E.; Fedoseyev, V.N. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Franberg, H. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Laboratory for Radio- and Environmental Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Joinet, A. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Centre d' Etude Spatiale des Rayonnements, 9 Av. du Colonel Roche, F-31028 Toulouse Cedex 4 (France); Jost, C. [HGF VISTARS and Institut fuer Kernchemie, Johannes-Gutenberg Universitaet Mainz, D-55128 Mainz (Germany); Kerkines, I.S.K. [Laboratory of Physical Chemistry, National and Kapodistrian University of Athens, Department of Chemistry, Zografou 157 71, GR (Greece); Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA 30322 (United States); Kirchner, R. [Gesellschaft fuer Schwerionenforschung, Planckstr. 1, D-64291 Darmstadt (Germany)

    2008-10-15

    The heart of every ISOL (isotope separation on-line) facility is its target and ion source system. Its efficiency, selectivity and rapidity is decisive for the production of intense and pure ion beams of short-lived isotopes. Recent progress in ISOL target and ion source technology is discussed at the examples of radioactive ion beams of exotic zinc and tin isotopes that were purified by isothermal chromatography and molecular sideband separation respectively. An outlook is given to which other elements these purification methods are applicable.

  14. Progress in ISOL target-ion source systems

    International Nuclear Information System (INIS)

    Koester, U.; Arndt, O.; Bouquerel, E.; Fedoseyev, V.N.; Franberg, H.; Joinet, A.; Jost, C.; Kerkines, I.S.K.; Kirchner, R.

    2008-01-01

    The heart of every ISOL (isotope separation on-line) facility is its target and ion source system. Its efficiency, selectivity and rapidity is decisive for the production of intense and pure ion beams of short-lived isotopes. Recent progress in ISOL target and ion source technology is discussed at the examples of radioactive ion beams of exotic zinc and tin isotopes that were purified by isothermal chromatography and molecular sideband separation respectively. An outlook is given to which other elements these purification methods are applicable.

  15. Far-infrared observations of M17: The interaction of an H II region with a molecular cloud

    International Nuclear Information System (INIS)

    Gatley, I.; Becklin, E.E.; Sellgren, K.; Werner, M.W.

    1979-01-01

    The central 15' of the M17 H II region--molecular cloud complex has been mapped with 1' resolution simultaneously at 30, 50, and 100 μm. The data suggest that the bulk of the luminosity radiated in the far-infrared is supplied by the exciting stars of the H II region; the far-infrared radiation is thermal emission from dust grains located chiefly outside the ionized gas. Large-scale systematic gradients in both the temperature and the column density of the dust are seen across the source. The appearance of the source in the far-infrared reflects the markedly nonuniform distribution of matter around the exciting stars; the H II region is bounded by the molecular cloud to the southwest. The core of the molecular cloud is heated primarily by infrared radiation from dust within and adjacent to the H II region; no evidence is seen for substantial luminosity sources embedded within the molecular cloud

  16. Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

    International Nuclear Information System (INIS)

    Ali, M. S.; Latif, Z.

    2016-01-01

    Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

  17. Molecular Epidemiologic Source Tracking of Orally Transmitted Chagas Disease, Venezuela

    Science.gov (United States)

    Segovia, Maikell; Martínez, Clara E.; Messenger, Louisa A.; Nessi, Anaibeth; Londoño, Juan C.; Espinosa, Raul; Martínez, Cinda; Alfredo, Mijares; Bonfante-Cabarcas, Rafael; Lewis, Michael D.; de Noya, Belkisyolé A.; Miles, Michael A.; Llewellyn, Martin S.

    2013-01-01

    Oral outbreaks of Chagas disease are increasingly reported in Latin America. The transitory presence of Trypanosoma cruzi parasites within contaminated foods, and the rapid consumption of those foods, precludes precise identification of outbreak origin. We report source attribution for 2 peri-urban oral outbreaks of Chagas disease in Venezuela via high resolution microsatellite typing. PMID:23768982

  18. Experimental Study of WBFC method for testing electromagnetic immunity of integrated circuits

    OpenAIRE

    香川, 直己; カガワ, ナオキ; Naoki, KAGAWA

    2004-01-01

    The author made a workbench faraday cage, WBFC, in order to estimate performance of the WBFC method for the measurement of common mode noise immunity of integrated circuits. In this report, characteristics of the constructed workbench faraday cage and results of experimental study of effects of the common mode noise on a circuit board including an electronic device are shown. Selected DUT, LM324 is popular operational amplifier for electrical circuits in vehicles.

  19. Cancer Stratification by Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Justus Weber

    2015-03-01

    Full Text Available The lack of specificity of traditional cytotoxic drugs has triggered the development of anticancer agents that selectively address specific molecular targets. An intrinsic property of these specialized drugs is their limited applicability for specific patient subgroups. Consequently, the generation of information about tumor characteristics is the key to exploit the potential of these drugs. Currently, cancer stratification relies on three approaches: Gene expression analysis and cancer proteomics, immunohistochemistry and molecular imaging. In order to enable the precise localization of functionally expressed targets, molecular imaging combines highly selective biomarkers and intense signal sources. Thus, cancer stratification and localization are performed simultaneously. Many cancer types are characterized by altered receptor expression, such as somatostatin receptors, folate receptors or Her2 (human epidermal growth factor receptor 2. Similar correlations are also known for a multitude of transporters, such as glucose transporters, amino acid transporters or hNIS (human sodium iodide symporter, as well as cell specific proteins, such as the prostate specific membrane antigen, integrins, and CD20. This review provides a comprehensive description of the methods, targets and agents used in molecular imaging, to outline their application for cancer stratification. Emphasis is placed on radiotracers which are used to identify altered expression patterns of cancer associated markers.

  20. Molecular outflows in the L1641 region of Orion

    International Nuclear Information System (INIS)

    Morgan, J.A.

    1990-01-01

    Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and molecular clouds were not mapped to sufficiently high spatial resolution to resolve the interaction. The interaction between molecular outflows and the L1641 molecular cloud is addressed by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point 12-CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The lack of an optical counterpart for many molecular outflows suggest that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation

  1. A recycling molecular beam reactor

    International Nuclear Information System (INIS)

    Prada-Silva, G.; Haller, G.L.; Fenn, J.B.

    1974-01-01

    In a Recycling Molecular Beam Reactor, RMBR, a beam of reactant gas molecules is formed from a supersonic free jet. After collision with a target the molecules pass through the vacuum pumps and are returned to the nozzle source. Continuous recycling permits the integration of very small reaction probabilities into measurable conversions which can be analyzed by gas chromatography. Some preliminary experiments have been carried out on the isomerization of cyclopropane

  2. 1978 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  3. Recommended rest frequencies for observed interstellar molecular transitions

    International Nuclear Information System (INIS)

    Lovas, F.J.; Snyder, I.E.; Johnson, D.R.

    1979-01-01

    The most accurate values presently available for the rest frequencies of all known interstellar molecular transitions are presented and recommended for reference in future astronomical observations in the radio and microwave regions. The recommended values have been carefully selected after critical evaluation of the spectroscopic literature. Probable error limits along with the proper molecular and quantum mechanical labels are presented for each observed transition. Representative line antenna temperatures are also presented for a typical source as a convenience to users. References are cited to both the astronomical and the laboratory literature

  4. 1979 bibliography of atomic and molecular processes. [Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  5. VLA OH Zeeman Observations of the NGC 6334 Complex Source A

    Science.gov (United States)

    Mayo, E. A.; Sarma, A. P.; Troland, T. H.; Abel, N. P.

    2004-12-01

    We present a detailed analysis of the NGC 6334 complex source A, a compact continuum source in the SW region of the complex. Our intent is to determine the significance of the magnetic field in the support of the surrounding molecular cloud against gravitational collapse. We have performed OH 1665 and 1667 MHz observations taken with the Very Large Array in the BnA configuration and combined these data with the lower resolution CnB data of Sarma et al. (2000). These observations reveal magnetic fields with values of the order of 350 μ G toward source A, with maximum fields reaching 500 μ G. We have also theoretically modeled the molecular cloud surrounding source A using Cloudy, with the constraints to the model based on observation. This model provides significant information on the density of H2 through the cloud and also the relative density of H2 to OH which is important to our analysis of the region. We will combine the knowledge gained through the Cloudy modeling with Virial estimates to determine the significance of the magnetic field to the dynamics and evolution of source A.

  6. Atomic and molecular physics of controlled thermonuclear fusion

    International Nuclear Information System (INIS)

    Joachain, C.J.; Post, D.E.

    1983-01-01

    This book attempts to provide a comprehensive introduction to the atomic and molecular physics of controlled thermonuclear fusion, and also a self-contained source from which to start a systematic study of the field. Presents an overview of fusion energy research, general principles of magnetic confinement, and general principles of inertial confinement. Discusses the calculation and measurement of atomic and molecular processes relevant to fusion, and the atomic and molecular physics of controlled thermonuclear research devices. Topics include recent progress in theoretical methods for atomic collisions; current theoretical techniques for electron-atom and electronion scattering; experimental aspects of electron impact ionization and excitation of positive ions; the theory of charge exchange and ionization by heavy particles; experiments on electron capture and ionization by multiply charged ions; Rydberg states; atomic and molecular processes in high temperature, low-density magnetically confined plasmas; atomic processes in high-density plasmas; the plasma boundary region and the role of atomic and molecular processes; neutral particle beam production and injection; spectroscopic plasma diagnostics; and particle diagnostics for magnetic fusion experiments

  7. Atomic and molecular excitation mechanisms in the interstellar medium

    International Nuclear Information System (INIS)

    Sternberg, A.

    1986-01-01

    The detailed infrared response of dense molecular hydrogen gas to intense ultraviolet radiation fields in photodissociation regions is presented. The thermal and chemical structures of photodissociation regions are analyzed, and the relationship between the emission by molecular hydrogen and trace atomic and molecular species is explored. The ultraviolet spectrum of radiation generated by cosmic rays inside dense molecular clouds is presented, and the resulting rates of photodissociation for a variety of interstellar molecules are calculated. Effects of this radiation on the chemistry of dense molecular clouds are discussed, and it is argued that the cosmic ray induced photons will significantly inhibit the production of complex molecular species. It is argued that the annihilation of electrons and positrons at the galactic center may result in observable infrared line emission by atomic hydrogen. A correlation between the intensity variations of the 511 keV line and the hydrogen infrared lines emitted by the annihilation region is predicted. The observed infrared fluxes from compact infrared sources at the galactic center may be used to constrain theories of pair production there

  8. Application of group analysis to the spatially homogeneous and isotropic Boltzmann equation with source using its Fourier image

    International Nuclear Information System (INIS)

    Grigoriev, Yurii N; Meleshko, Sergey V; Suriyawichitseranee, Amornrat

    2015-01-01

    Group analysis of the spatially homogeneous and molecular energy dependent Boltzmann equations with source term is carried out. The Fourier transform of the Boltzmann equation with respect to the molecular velocity variable is considered. The correspondent determining equation of the admitted Lie group is reduced to a partial differential equation for the admitted source. The latter equation is analyzed by an algebraic method. A complete group classification of the Fourier transform of the Boltzmann equation with respect to a source function is given. The representation of invariant solutions and corresponding reduced equations for all obtained source functions are also presented. (paper)

  9. Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams.

    Science.gov (United States)

    Gordin, Alexander; Fialkov, Alexander B; Amirav, Aviv

    2008-09-01

    A major benefit of gas chromatography/mass spectrometry (GC/MS) with a supersonic molecular beam (SMB) interface and its fly-through ion source is the ability to obtain electron ionization of vibrationally cold molecules (cold EI), which show enhanced molecular ions. However, GC/MS with an SMB also has the flexibility to perform 'classical EI' mode of operation which provides mass spectra to mimic those in commercial 70 eV electron ionization MS libraries. Classical EI in SMB is obtained through simple reduction of the helium make-up gas flow rate, which reduces the SMB cooling efficiency; hence the vibrational temperatures of the molecules are similar to those in traditional EI ion sources. In classical EI-SMB mode, the relative abundance of the molecular ion can be tuned and, as a result, excellent identification probabilities and very good matching factors to the NIST MS library are obtained. Classical EI-SMB with the fly-through dual cage ion source has analyte sensitivity similar to that of the standard EI ion source of a basic GC/MS system. The fly-through EI ion source in combination with the SMB interface can serve for cold EI, classical EI-SMB, and cluster chemical ionization (CCI) modes of operation, all easily exchangeable through a simple and quick change (not involving hardware). Furthermore, the fly-through ion source eliminates sample scattering from the walls of the ion source, and thus it offers full sample inertness, tailing-free operation, and no ion-molecule reaction interferences. It is also robust and enables increased column flow rate capability without affecting the sensitivity.

  10. NEWLY IDENTIFIED EXTENDED GREEN OBJECTS (EGOs) FROM THE SPITZER GLIMPSE II SURVEY. II. MOLECULAR CLOUD ENVIRONMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Chen Xi; Gan Conggui; Shen Zhiqiang [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030 (China); Ellingsen, Simon P.; Titmarsh, Anita [School of Mathematics and Physics, University of Tasmania, Hobart, Tasmania (Australia); He Jinhua, E-mail: chenxi@shao.ac.cn [Key Laboratory for the Structure and Evolution of Celestial Objects, Yunnan Astronomical Observatory/National Astronomical Observatory, Chinese Academy of Sciences, P.O. Box 110, Kunming 650011, Yunnan Province (China)

    2013-06-01

    We have undertaken a survey of molecular lines in the 3 mm band toward 57 young stellar objects using the Australia Telescope National Facility Mopra 22 m radio telescope. The target sources were young stellar objects with active outflows (extended green objects (EGOs)) newly identified from the GLIMPSE II survey. We observe a high detection rate (50%) of broad line wing emission in the HNC and CS thermal lines, which combined with the high detection rate of class I methanol masers toward these sources (reported in Paper I) further demonstrates that the GLIMPSE II EGOs are associated with outflows. The physical and kinematic characteristics derived from the 3 mm molecular lines for these newly identified EGOs are consistent with these sources being massive young stellar objects with ongoing outflow activity and rapid accretion. These findings support our previous investigations of the mid-infrared properties of these sources and their association with other star formation tracers (e.g., infrared dark clouds, methanol masers and millimeter dust sources) presented in Paper I. The high detection rate (64%) of the hot core tracer CH{sub 3}CN reveals that the majority of these new EGOs have evolved to the hot molecular core stage. Comparison of the observed molecular column densities with predictions from hot core chemistry models reveals that the newly identified EGOs from the GLIMPSE II survey are members of the youngest hot core population, with an evolutionary time scale of the order of 10{sup 3} yr.

  11. Microtron MT 25 as a source of neutrons

    Czech Academy of Sciences Publication Activity Database

    Králík, M.; Šolc, J.; Chvátil, David; Krist, Pavel; Turek, Karel; Granja, C.

    2012-01-01

    Roč. 83, č. 8 (2012), 083502/1-083502/7 ISSN 0034-6748 Grant - others:ESA(XE) 22908/09/NL/CBi Institutional support: RVO:61389005 Keywords : neutron source * microtron Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.602, year: 2012

  12. The use of molecular chemistry (pyrolysis-GC/MS) in the environmental interpretation of peat

    NARCIS (Netherlands)

    Schellekens, J.

    2013-01-01

      The molecular composition of organic matter in peatlands reflects local conditions and stores information about botanical composition (plant source) as well as the degree of and conditions during decomposition. A reliable hydrological (and hence palaeoclimatological) interpretation of source

  13. Springer handbook of atomic, molecular, and optical physics

    CERN Document Server

    Cassar, Mark M

    2006-01-01

    This Springer Handbook of Atomic, Molecular, and Optical Physics comprises a comprehensive reference source that unifies the entire fields of atomic, molecular, and optical (AMO) physics, assembling the principal ideas, techniques and results of the field from atomic spectroscopy to applications in comets. Its 92 chapters are written by over 100 authors, all leaders in their respective disciplines. Carefully edited to ensure uniform coverage and style, with extensive cross references, and acting as a guide to the primary research literature, it is both a source of information and an inspiration for graduate students and other researchers new to the field. Relevant diagrams, graphs, and tables of data are provided throughout the text. Substantially updated and expanded since the 1996 edition and published in conjunction with the 2005 World Year of Physics (commemorating Einstein’s 1905 "miracle year"), it contains several entirely new chapters covering current areas of great research interest, such as Bose �...

  14. Plant-aphid interactions: molecular and ecological perspectives.

    Science.gov (United States)

    Goggin, Fiona L

    2007-08-01

    Many aphids are major agricultural pests because of their unparalleled reproductive capacity and their ability to manipulate host plant physiology. Aphid population growth and its impact on plant fitness are strongly influenced by interactions with other organisms, including plant pathogens, endophytes, aphid endosymbionts, predators, parasitoids, ants, and other herbivores. Numerous molecular and genomic resources have recently been developed to identify sources of aphid resistance in plants, as well as potentially novel targets for control in aphids. Moreover, the same model systems that are used to explore direct molecular interactions between plants and aphids can be utilized to study the ecological context in which they occur.

  15. Apportioning sources of organic matter in streambed sediments: An integrated molecular and compound-specific stable isotope approach

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, Richard J., E-mail: Richard.J.Cooper@uea.ac.uk [School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ (United Kingdom); Pedentchouk, Nikolai; Hiscock, Kevin M.; Disdle, Paul [School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ (United Kingdom); Krueger, Tobias [IRI THESys, Humboldt University, 10099 Berlin (Germany); Rawlins, Barry G. [British Geological Survey, Keyworth, Nottingham NG12 5GG (United Kingdom)

    2015-07-01

    We present a novel application for quantitatively apportioning sources of organic matter in streambed sediments via a coupled molecular and compound-specific isotope analysis (CSIA) of long-chain leaf wax n-alkane biomarkers using a Bayesian mixing model. Leaf wax extracts of 13 plant species were collected from across two environments (aquatic and terrestrial) and four plant functional types (trees, herbaceous perennials, and C{sub 3} and C{sub 4} graminoids) from the agricultural River Wensum catchment, UK. Seven isotopic (δ{sup 13}C{sub 27}, δ{sup 13}C{sub 29}, δ{sup 13}C{sub 31}, δ{sup 13}C{sub 27–31}, δ{sup 2}H{sub 27}, δ{sup 2}H{sub 29}, and δ{sup 2}H{sub 27–29}) and two n-alkane ratio (average chain length (ACL), carbon preference index (CPI)) fingerprints were derived, which successfully differentiated 93% of individual plant specimens by plant functional type. The δ{sup 2}H values were the strongest discriminators of plants originating from different functional groups, with trees (δ{sup 2}H{sub 27–29} = − 208‰ to − 164‰) and C{sub 3} graminoids (δ{sup 2}H{sub 27–29} = − 259‰ to − 221‰) providing the largest contrasts. The δ{sup 13}C values provided strong discrimination between C{sub 3} (δ{sup 13}C{sub 27–31} = − 37.5‰ to − 33.8‰) and C{sub 4} (δ{sup 13}C{sub 27–31} = − 23.5‰ to − 23.1‰) plants, but neither δ{sup 13}C nor δ{sup 2}H values could uniquely differentiate aquatic and terrestrial species, emphasizing a stronger plant physiological/biochemical rather than environmental control over isotopic differences. ACL and CPI complemented isotopic discrimination, with significantly longer chain lengths recorded for trees and terrestrial plants compared with herbaceous perennials and aquatic species, respectively. Application of a comprehensive Bayesian mixing model for 18 streambed sediments collected between September 2013 and March 2014 revealed considerable temporal variability in the

  16. Energetic molecular outflow near AFGL 961: millimeter-wave and infrared observations

    International Nuclear Information System (INIS)

    Lada, C.J.; Gautier, T.N. III

    1982-01-01

    We report detailed millimeter-wave and near-infrared spectroscopy of the dynamically active region around the infrared source AFGL 961, near the Rosette nebula. Millimeter-wave 12 CO observations are used to study the high-velocity molecular flow around AFGL 961. These observations show that the high-velocity flow has a maximum extent of at least 6' or 2.9 pc at the distance of AFGL 961. The flow is found to be anisotropic, with redshifted high-velocity emission considerably more extended than blueshifted high-velocity emission. However, the flow does not appear to be as highly collimated as some other sources of high-velocity bipolar outflow. We also find the emission profiles to be asymmetric in velocity such that the integrated intensity of the redshifted high-velocity emission is on average 2.5 times greater than that of the blueshifted emission. The mass of the gas involved in the flow is determined to be approximately 19 M/sub sun/, and the kinetic energy of this gas is estimated to be about 8 x 10 46 ergs. These observations are interpreted as evidence that an energetic bipolar outflow of molecular gas is occurring near AFGL 961. The momentum of the outflowing molecular gas is large, and it is shown that this places strong constraints on possible physical mechanisms which may be driving the outflow. The near-infrared spectrum of AFGL 961 from 1.4-2.4 μm was obtained in order to study the conditions immediately around the infrared source which may be driving the molecular outflow

  17. Microbial source tracking: a tool for identifying sources of microbial contamination in the food chain.

    Science.gov (United States)

    Fu, Ling-Lin; Li, Jian-Rong

    2014-01-01

    The ability to trace fecal indicators and food-borne pathogens to the point of origin has major ramifications for food industry, food regulatory agencies, and public health. Such information would enable food producers and processors to better understand sources of contamination and thereby take corrective actions to prevent transmission. Microbial source tracking (MST), which currently is largely focused on determining sources of fecal contamination in waterways, is also providing the scientific community tools for tracking both fecal bacteria and food-borne pathogens contamination in the food chain. Approaches to MST are commonly classified as library-dependent methods (LDMs) or library-independent methods (LIMs). These tools will have widespread applications, including the use for regulatory compliance, pollution remediation, and risk assessment. These tools will reduce the incidence of illness associated with food and water. Our aim in this review is to highlight the use of molecular MST methods in application to understanding the source and transmission of food-borne pathogens. Moreover, the future directions of MST research are also discussed.

  18. Nearby Hot Stars May Change Our View of Distant Sources

    Science.gov (United States)

    Kohler, Susanna

    2017-07-01

    As if it werent enough that quasars distant and bright nuclei of galaxies twinkle of their own accord due to internal processes, nature also provides another complication: these distant radio sources can also appear to twinkle because of intervening material between them and us. A new study has identified a possible source for the material getting in the way.Unexplained VariabilityA Spitzer infrared view of the Helix nebula, which contains ionized streamers of gas extending radially outward from the central star. [NASA/JPL-Caltech/Univ. of Ariz.]Distant quasars occasionally display extreme scintillation, twinkling with variability timescales shorter than a day. This intra-day variability is much greater than we can account for with standard models of the interstellar medium lying between the quasar and us. So what could cause this extreme scattering instead?The first clue to this mystery came from the discovery of strong variability in the radio source PKS 1322110. In setting up follow-up observations of this object, Mark Walker (Manly Astrophysics, Australia) and collaborators noticed that, in the plane of the sky, PKS 1322110 lies very near the bright star Spica. Could this be coincidence, or might this bright foreground star have something to do with the extreme scattering observed?Diagram explaining the source of the intra-day radio source variability as intervening filaments surrounding a hot star. [M. Walker/CSIRO/Manly Astrophysics]Swarms of ClumpsWalker and collaborators put forward a hypothesis: perhaps the ultraviolet photons of nearby hot stars ionize plasma around them, which in turn causes the extreme scattering of the distant background sources.As a model, the authors consider the Helix Nebula, in which a hot, evolved star is surrounded by cool globules of molecular hydrogen gas. The radiation from the star hits these molecular clumps, dragging them into long radial streamers and ionizing their outer skins.Though the molecular clumps in the Helix

  19. Use of molecular markers in plant breeding = [Het gebruik van moleculaire merkers in de plantenveredeling

    NARCIS (Netherlands)

    Berloo, van R.

    2000-01-01

    Molecular markers provide plant breeding with an important and valuable new source of information. Linkage between molecular markers can be translated to genetic linkage maps, which have become an important tool in plant and animal genetics. Linkage between (quantitative) trait-data and

  20. The future of nanofabrication and molecular scale devices in nanomedicine.

    Science.gov (United States)

    Freitas, R A

    2002-01-01

    Nanotechnology is engineering and manufacturing at the molecular scale, and the application of nanotechnology to medicine is called nanomedicine. Nanomedicine subsumes three mutually overlapping and progressively more powerful molecular technologies. First, nanoscale-structured materials and devices that can be fabricated today hold great promise for advanced diagnostics and biosensors, targeted drug delivery and smart drugs, and immunoisolation therapies. Second, biotechnology offers the benefits of molecular medicine via genomics, proteomics, and artificial engineered microbes. Third, in the longer term, molecular machine systems and medical nanorobots will allow instant pathogen diagnosis and extermination, chromosome replacement and individual cell surgery in vivo, and the efficient augmentation and improvement of natural physiological function. Current research is exploring the fabrication of designed nanostructures, nanoactuators and nanomotors, microscopic energy sources, and nanocomputers at the molecular scale, along with the means to assemble them into larger systems, economically and in great numbers.

  1. Molecular simulation of the thermophysical properties of N-functionalized alkylimidazoles.

    Science.gov (United States)

    Turner, C Heath; Cooper, Alex; Zhang, Zhongtao; Shannon, Matthew S; Bara, Jason E

    2012-06-07

    Molecular simulations are used to probe the thermophysical properties of a series of N-functionalized alkylimidazoles, ranging from N-methylimidazole to N-heptylimidazole. These compounds have been previously synthesized, and their solvation properties have been shown to be potentially useful for CO(2) capture from industrial sources. In this work, we use first-principles calculations to fit electrostatic charges to the molecular models, which are then used to perform a series of molecular dynamics simulations. Over a range of different temperatures, we benchmark the simulated densities and heat capacities against experimental measurements. Also, we predict the Henry's constants for CO(2) absorption and probe the solvents' structures using molecular simulation techniques, such as fractional free volume analysis and void distributions. We find that our simulations are able to closely reproduce the experimental benchmarks and add additional insight into the molecular structure of these fluids, with respect to their observed solvent properties.

  2. eMovie: a storyboard-based tool for making molecular movies.

    Science.gov (United States)

    Hodis, Eran; Schreiber, Gideon; Rother, Kristian; Sussman, Joel L

    2007-05-01

    The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy molecular animations much easier. This tool is a plug-in for the open-source molecular graphics program PyMOL, and enables experts and novices alike to produce informative and high-quality molecular animations.

  3. Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

    Science.gov (United States)

    Dizkirici, Ayten; Tekpinar, Mustafa

    2015-03-01

    GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

  4. Principal and experimental study of source of polarized electrons

    International Nuclear Information System (INIS)

    Shang Rencheng; Gao Junfang; Xiao Yuan; Pang Wenning; Deng Jingkang

    1999-01-01

    The getting of polarized electrons was briefly introduced, that is the source of polarized electrons. The measurement of polarization in future, the application of polarized electrons in atomic and molecular physics, condensed physics, biological physics, nuclear and particle physics were discussed

  5. Optical laser systems at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Minitti, Michael P.; Robinson, Joseph S.; Coffee, Ryan N.; Edstrom, Steve; Gilevich, Sasha; Glownia, James M.; Granados, Eduardo; Hering, Philippe; Hoffmann, Matthias C.; Miahnahri, Alan; Milathianaki, Despina; Polzin, Wayne; Ratner, Daniel; Tavella, Franz; Vetter, Sharon; Welch, Marc; White, William E.; Fry, Alan R., E-mail: alanfry@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-22

    This manuscript serves as a reference to describe the optical laser sources and capabilities at the Linac Coherent Light Source. Ultrafast optical lasers play an essential role in exploiting the unique capabilities of recently commissioned X-ray free-electron laser facilities such as the Linac Coherent Light Source (LCLS). Pump–probe experimental techniques reveal ultrafast dynamics in atomic and molecular processes and reveal new insights in chemistry, biology, material science and high-energy-density physics. This manuscript describes the laser systems and experimental methods that enable cutting-edge optical laser/X-ray pump–probe experiments to be performed at LCLS.

  6. New CO and HCN sources associated with IRAS carbon stars

    Science.gov (United States)

    NGUYEN-Q-RIEU; Epchtein, N.; TRUONG-BACH; Cohen, M.

    1987-01-01

    Emission of CO and HCN was detected in 22 out of a sample of 53 IRAS sources classified as unidentified carbon-rich objects. The sample was selected according to the presence of the silicon carbide feature as revealed by low-resolution spectra. The molecular line widths indicate that the CO and HCN emission arises from the circumstellar envelopes of very highly evolved stars undergoing mass loss. The visible stars tend to be deficient in CO as compared with unidentified sources. Most the detected CO and HCN IRAS stars are distinct and thick-shelled objects, but their infrared and CO luminosities are similar to those of IRC + 102156 AFGL and IRC-CO evolved stars. The 12 micron flux seems to be a good indicator of the distance, hence a guide for molecular searches.

  7. The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

    Science.gov (United States)

    Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

    2013-07-01

    The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

  8. Long Carbon Chains in the Warm Carbon-chain-chemistry Source L1527: First Detection of C7H in Molecular Clouds

    Science.gov (United States)

    Araki, Mitsunori; Takano, Shuro; Sakai, Nami; Yamamoto, Satoshi; Oyama, Takahiro; Kuze, Nobuhiko; Tsukiyama, Koichi

    2017-09-01

    Long carbon-chain molecules were searched for toward the low-mass star-forming region L1527, which is a prototypical source of warm carbon-chain chemistry (WCCC), using the 100 m Green Bank Telescope. Long carbon-chain molecules, C7H (2Π1/2), C6H (2Π3/2 and 2Π1/2), CH3C4H, and C6H2 (cumulene carbene, CCCCCCH2), and cyclic species of C3H and C3H2O were detected. In particular, C7H was detected for the first time in molecular clouds. The column density of C7H is determined to be 6 × 1010 cm-2. The column densities of the carbon-chain molecules including CH3C4H and C6H in L1527 relative to those in the starless dark cloud Taurus Molecular Cloud-1 Cyanopolyyne Peak (TMC-1 CP) tend to be systematically lower for long carbon-chain lengths. However, the column densities of C7H and C6H2 do not follow this trend and are found to be relatively abundant in L1527. This result implies that these long carbon-chain molecules are remnants of the cold starless phase. The results—that both the remnants and WCCC products are observed toward L1527—are consistent with the suggestion that the protostar can also be born in the parent core at a relatively early stage in the chemical evolution.

  9. Molecular DNA identification of blood sources fed on, for Culicine mosquitoes (Diptera: Culicidae collected in the Songkhla province, southern Thailand

    Directory of Open Access Journals (Sweden)

    Theerakamol Pengsakul

    2017-12-01

    Full Text Available Culicine mosquitoes are medically important vectors. Therefore, mosquito control measures are a crucial strategy to interrupt disease transmission. Collection of data on mosquito feeding patterns is crucial for developing an effective vector control strategy. The objective of this study was to use molecular biology methods to identify the sources of DNA in mosquito blood meals. The DNA from blood meals in the mosquito stomachs was extracted and amplified with multiplex PCR, using specific primer sets based on the mitochondrial cytochrome b gene, to identify the DNA sources among human, pig, goat, dog, cow, and chicken. Among the 297 mosquito samples collected in the Songkhla province of Thailand, in Aedes spp. mosquitoes the percentages positive for human, dog, pig, chicken, cow, a mixture of 2 vertebrate DNAs, or of 3, and negative (no identified DNA were 61.90, 2.38, 2.38, 0.60, 0.60, 4.18, 1.20 and 26.79% respectively. In Culex spp. blood meals the rank order was different: fractions positive for chicken, human, dog, cow, goat, pig, a mixture of 2 or 3 vertebrate DNAs, and negative were 40.83, 10.00, 5.00, 4.17, 1.67, 0.83, 8.32, 3.32 and 25.83% respectively. This study shows that feeding behaviors of the two species differ, with most Aedes spp. blood meals containing human blood, while Culex spp. had primarily consumed chicken blood. An improved understanding of the feeding behaviors of mosquitoes could contribute to new, more effective strategies for the control of mosquito populations.

  10. Determination of Chlorine in Milk via Molecular Absorption of SrCl Using High-Resolution Continuum Source Graphite Furnace Atomic Absorption Spectrometry.

    Science.gov (United States)

    Ozbek, Nil; Akman, Suleyman

    2016-07-20

    Total chlorine in milk was determined via the molecular absorption of diatomic strontium monochloride at 635.862 nm using high-resolution continuum source graphite furnace atomic absorption spectrometry. The effects of coating the graphite furnace, using different modifiers, amount of molecule-forming element, and different calibrants were investigated and optimized. Chlorine concentrations in milk samples were determined in a Zr-coated graphite furnace using 25 μg of Sr as the molecule-forming reagent and applying a pyrolysis temperature of 600 °C and a molecule-forming temperature of 2300 °C. Linearity was maintained up to 500 μg mL(-1) of Cl. The method was tested by analyzing a certified reference wastewater. The results were in the uncertainty limits of the certified value. The limit of detection of the method was 1.76 μg mL(-1). The chlorine concentrations in various cow milk samples taken from the market were found in the range of 588-1472 mg L(-1).

  11. Atomic physics at high brilliance synchrotron sources: Proceedings

    International Nuclear Information System (INIS)

    Berry, G.; Cowan, P.; Gemmell, D.

    1994-08-01

    This report contains papers on the following topics: present status of SPring-8 and the atomic physics undulator beamline; recent photoabsorption measurements in the rare gases and alkalis in the 3 to 15 keV proton energy region; atomic and molecular physics at LURE; experiments on atoms, ions and small molecules using the new generation of synchrotron radiation sources; soft x-ray fluorescence spectroscopy using tunable synchrotron radiation; soft x-ray fluorescence spectroscopy excited by synchrotron radiation: Inelastic and resonant scattering near threshold; outer-shell photoionization of ions; overview of the APS BESSRC beamline development; the advanced light source: Research opportunities in atomic and molecular physics; Photoionization of the Ba + ion by 4d shell excitation; decay dynamics of inner-shell excited atoms and molecules; absorption of atomic Ca, Cr, Mn and Cu; High-resolution photoelectron studies of resonant molecular photoionization; radiative and radiationless resonant raman scattering by synchrotron radiation; auger spectrometry of atoms and molecules; some thoughts of future experiments with the new generation of storage rings; Electron spectroscopy studies of argon K-shell excitation and vacancy cascades; ionization of atoms by high energy photons; ion coincidence spectroscopy on rare gas atoms and small molecules after photoexcitation at energies of several keV; an EBIS for use with synchrotron radiation photoionization of multiply charged ions and PHOBIS; gamma-2e coincidence measurements the wave of the future in inner-shell electron spectroscopy; recoil momentum spectroscopy in ion-atom and photon-atom collisions; a study of compton ionization of helium; future perspectives of photoionization studies at high photon energies; and status report on the advanced photon source. These papers have been cataloged separately elsewhere

  12. Fate of PCBs, PAHs and their source characteristic ratios during composting and digestion of source-separated organic waste in full-scale plants

    International Nuclear Information System (INIS)

    Braendli, Rahel C.; Bucheli, Thomas D.; Kupper, Thomas; Mayer, Jochen; Stadelmann, Franz X.; Tarradellas, Joseph

    2007-01-01

    Composting and digestion are important waste management strategies. However, the resulting products can contain significant amounts of organic pollutants such as polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs). In this study we followed the concentration changes of PCBs and PAHs during composting and digestion on field-scale for the first time. Concentrations of low-chlorinated PCBs increased during composting (about 30%), whereas a slight decrease was observed for the higher chlorinated congeners (about 10%). Enantiomeric fractions of atropisomeric PCBs were essentially racemic and stable over time. Levels of low-molecular-weight PAHs declined during composting (50-90% reduction), whereas high-molecular-weight compounds were stable. The PCBs and PAHs concentrations did not seem to vary during digestion. Source apportionment by applying characteristic PAH ratios and molecular markers in input material did not give any clear results. Some of these parameters changed considerably during composting. Hence, their diagnostic potential for finished compost must be questioned. - During field-scale composting, low molecular weight PCBs and PAHs increased and decreased, respectively, whereas high molecular weight compounds remained stable

  13. Experimental methods in radioactive ion-beam target/ion source development and characterization

    International Nuclear Information System (INIS)

    Welton, R.F.; Alton, G.D.; Cui, B.; Murray, S.N.

    1998-01-01

    We have developed off-line experimental techniques and apparatuses that permit direct measurement of effusive-flow delay times and ionization efficiencies for nearly any chemically reactive element in high-temperature target/ion sources (TIS) commonly used for on-line radioactive ion-beam (RIB) generation. The apparatuses include a hot Ta valve for effusive-flow delay-time measurements, a cooled molecular injection system for determination of ionization efficiencies, and a gas flow measurement/control system for introducing very low, well-defined molecular flows into the TIS. Measurements are performed on a test stand using molecular feed compounds containing stable complements of the radioactive nuclei of interest delivered to the TIS at flow rates commensurate with on-line RIB generation. In this article, the general techniques are described and effusive-flow delay times and ionization efficiency measurements are reported for fluorine in an electron-beam plasma target/ion source developed for RIB generation and operated in both positive- and negative-ion extraction modes. copyright 1998 American Institute of Physics

  14. Proceedings of the workshop on characterization of molecular assemblies

    International Nuclear Information System (INIS)

    Imae, Toyoko; Furusaka, Michihiro

    1993-08-01

    Molecular condensation system shows the different physical characteristic properties from those of the component molecules, therefore, this workshop was to offer the place of discussion on the future of the research on molecular assembly state from wide visual field. The workshop was held on March 15 and 16, 1993 at the National Laboratory for High Energy Physics (KEK). Lectures were given on future plan of pulsed neutron sources and present state of Wink, characterization by small angle neutron scattering of molecular assemblies that dodecyl dimethylamine oxide constructs, microscopic and macroscopic structures of new surface active molecules, characterization of phospholipid molecular assembly state, crystalline molecular complex formed in surfactant and additives, small angle neutron scattering for phase separation and critical phenomena of micro-emulsion, structural research on hydrophilic composite lipid, associative behavior of bile acid salts in aqueous solution, phase separation and morphology of surfactant system, characterization of macroscopic structure in polymers by ultrasmall angle X-ray scattering and dynamic light scattering, and research on light scattering of glass-forming polymers. (K.I.)

  15. Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

    Directory of Open Access Journals (Sweden)

    Shahram Radei

    2018-02-01

    Full Text Available This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100 °C. Moreover, the dyeing rate constants, correlation coefficient and activation energies were proposed for this system. It was found that o-vanillin yielded higher dye absorption levels than coumarin, leading to exhaustions of 88% and 87% for Disperse Red 167 and Disperse Blue 79, respectively. K/S values of dyed polyester were also found to be higher for dye baths containing o-vanillin with respect to the ones with coumarin. In terms of hot pressing fastness and wash fastness, generally no adverse influence on fastness properties was reported, while o-vanillin showed slightly better results compared to coumarin.

  16. Mini-review: Molecular mechanisms of antifouling compounds

    KAUST Repository

    Qian, Pei-Yuan

    2013-04-01

    Various antifouling (AF) coatings have been developed to protect submerged surfaces by deterring the settlement of the colonizing stages of fouling organisms. A review of the literature shows that effective AF compounds with specific targets are ones often considered non-toxic. Such compounds act variously on ion channels, quorum sensing systems, neurotransmitters, production/release of adhesive, and specific enzymes that regulate energy production or primary metabolism. In contrast, AF compounds with general targets may or may not act through toxic mechanisms. These compounds affect a variety of biological activities including algal photosynthesis, energy production, stress responses, genotoxic damage, immunosuppressed protein expression, oxidation, neurotransmission, surface chemistry, the formation of biofilms, and adhesive production/release. Among all the targets, adhesive production/release is the most common, possibly due to a more extensive research effort in this area. Overall, the specific molecular targets and the molecular mechanisms of most AF compounds have not been identified. Thus, the information available is insufficient to draw firm conclusions about the types of molecular targets to be used as sensitive biomarkers for future design and screening of compounds with AF potential. In this review, the relevant advantages and disadvantages of the molecular tools available for studying the molecular targets of AF compounds are highlighted briefly and the molecular mechanisms of the AF compounds, which are largely a source of speculation in the literature, are discussed. © 2013 Copyright Taylor and Francis Group, LLC.

  17. Rotational Laser Cooling of Vibrationally and Translationally Cold Molecular Ions

    DEFF Research Database (Denmark)

    Drewsen, Michael

    2011-01-01

    an excellent alternative to atomic qubits in the realization of a practical ion trap based quantum computer due to favourable internal state decoherence rates. In chemistry, state prepared molecular targets are an ideal starting point for uni-molecular reactions, including coherent control...... of photofragmentation through the application of various laser sources [5,6]. In cold bi-molecular reactions, where the effect of even tiny potential barriers becomes significant, experiments with state prepared molecules can yield important information on the details of the potential curves of the molecular complexes...... by sympathetic cooling with Doppler laser cooled Mg+ ions. Giving the time for the molecules to equilibrate internally to the room temperature blackbody radiation, the vibrational degree of freedom will freeze out, leaving only the rotational degree of freedom to be cooled. We report here on the implementation...

  18. Classification of light sources and their interaction with active and passive environments

    Science.gov (United States)

    El-Dardiry, Ramy G. S.; Faez, Sanli; Lagendijk, Ad

    2011-03-01

    Emission from a molecular light source depends on its optical and chemical environment. This dependence is different for various sources. We present a general classification in terms of constant-amplitude and constant-power sources. Using this classification, we have described the response to both changes in the local density of states and stimulated emission. The unforeseen consequences of this classification are illustrated for photonic studies by random laser experiments and are in good agreement with our correspondingly developed theory. Our results require a revision of studies on sources in complex media.

  19. Classification of light sources and their interaction with active and passive environments

    International Nuclear Information System (INIS)

    El-Dardiry, Ramy G. S.; Faez, Sanli; Lagendijk, Ad

    2011-01-01

    Emission from a molecular light source depends on its optical and chemical environment. This dependence is different for various sources. We present a general classification in terms of constant-amplitude and constant-power sources. Using this classification, we have described the response to both changes in the local density of states and stimulated emission. The unforeseen consequences of this classification are illustrated for photonic studies by random laser experiments and are in good agreement with our correspondingly developed theory. Our results require a revision of studies on sources in complex media.

  20. Extended Hu¨ckel Calculations on Solids Using the Avogadro Molecular Editor and Visualizer

    Science.gov (United States)

    Avery, Patrick; Ludoweig, Herbert; Autschbach, Jochen; Zurek, Eva

    2018-01-01

    The "Yet Another extended Hu¨ckel Molecular Orbital Package" (YAeHMOP) has been merged with the Avogadro open-source molecular editor and visualizer. It is now possible to perform YAeHMOP calculations directly from the Avogadro graphical user interface for materials that are periodic in one, two, or three dimensions, and to visualize…

  1. Linking the Molecular Signature of Heteroatomic Dissolved Organic Matter to Watershed Characteristics in World Rivers.

    Science.gov (United States)

    Wagner, Sasha; Riedel, Thomas; Niggemann, Jutta; Vähätalo, Anssi V; Dittmar, Thorsten; Jaffé, Rudolf

    2015-12-01

    Large world rivers are significant sources of dissolved organic matter (DOM) to the oceans. Watershed geomorphology and land use can drive the quality and reactivity of DOM. Determining the molecular composition of riverine DOM is essential for understanding its source, mobility and fate across landscapes. In this study, DOM from the main stem of 10 global rivers covering a wide climatic range and land use features was molecularly characterized via ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). FT-ICR mass spectral data revealed an overall similarity in molecular components among the rivers. However, when focusing specifically on the contribution of nonoxygen heteroatomic molecular formulas (CHON, CHOS, CHOP, etc.) to the bulk molecular signature, patterns relating DOM composition and watershed land use became apparent. Greater abundances of N- and S-containing molecular formulas were identified as unique to rivers influenced by anthropogenic inputs, whereas rivers with primarily forested watersheds had DOM signatures relatively depleted in heteroatomic content. A strong correlation between cropland cover and dissolved black nitrogen was established when focusing specifically on the pyrogenic class of compounds. This study demonstrated how changes in land use directly affect downstream DOM quality and could impact C and nutrient cycling on a global scale.

  2. Inner Source Pickup Ions Observed by Ulysses

    Science.gov (United States)

    Gloeckler, G.

    2016-12-01

    The existence of an inner source of pickup ions close to the Sun was proposed in order to explain the unexpected discovery of C+ in the high-speed polar solar wind. Here I report on detailed analyses of the composition and the radial and latitudinal variations of inner source pickup ions measured with the Solar Wind Ion Composition Spectrometer on Ulysses from 1991 to 1998, approaching and during solar minimum. We find that the C+ intensity drops off with radial distance R as R-1.53, peaks at mid latitudes and drops to its lowest value in the ecliptic. Not only was C+ observed, but also N+, O+, Ne+, Na+, Mg+, Ar+, S+, K+, CH+, NH+, OH+, H2O+, H3O+, MgH+, HCN+, C2H4+, SO+ and many other singly-charged heavy ions and molecular ions. The measured velocity distributions of inner source pickup C+ and O+ indicate that these inner source pickup ions are most likely produced by charge exchange, photoionization and electron impact ionization of neutrals close to the Sun (within 10 to 30 solar radii). Possible causes for the unexpected latitudinal variations and the neutral source(s) producing the inner source pickup ions as well as plausible production mechanisms for inner source pickup ions will be discussed.

  3. Molecular beam sampling of a hollow cathode arc

    International Nuclear Information System (INIS)

    Theuws, P.

    1981-01-01

    This thesis deals with the description of the process of molecular beam sampling of a Hollow Cathode Arc. The aim of the study is twofold, i.e. investigation of the applicability of molecular beam sampling as a plasma diagnostic and the use of a Hollow Cathode Arc as a high intensity beam source for ground state atoms and metastable state atoms in the superthermal energy range. Suitable models are introduced, describing the process of molecular beam sampling of both ground state atoms and metastable state atoms. Fast ground state atoms produced by ion-atom collisions. The experimental facilities, i.e. the Hollow Cathode Arc, the time-of-flight machine and the dye laser system are described. And an alternative detection scheme for ground state atoms is presented and experimental results on the molecular beam sampling of a low density plasma (densities 10 19 -10 20 m -3 ) in the long arc configuration are reported. The results on the short arc configuration (densities 10 21 -10 22 m -3 ) are discussed. (Auth.)

  4. Molecular Diagnostic Tests for Microsporidia

    Directory of Open Access Journals (Sweden)

    Kaya Ghosh

    2009-01-01

    Full Text Available The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans.

  5. Russian Virtual Observatory: Data Sources

    Directory of Open Access Journals (Sweden)

    Malkov O.

    2016-03-01

    Full Text Available The purpose of this review is to analyze main directions of creation and functioning of major data sources developed by Russian astronomers or with their participation and to compare them with the worldwide trends in these fields. We discuss astronomical space missions of the past, present, and future (Astron, INTEGRAL, WSO-UV, Spectrum Roentgen Gamma, Lyra-B, high-quality photometric atlases and catalogues, and spectroscopic data sources, primarily VALD and the global VAMDC framework for the maintenance and distribution of atomic and molecular data. We describe collection, analysis, and dissemination of astronomical data on minor bodies of the Solar System and on variable stars. Also described is the project joining data for all observational types of binary and multiple stars, Binary star DataBase (BDB.

  6. Molecular beams with extremely narrow velocity spreads from free jet expansions

    International Nuclear Information System (INIS)

    Buck, U.; Dueker, M.; Pauly, H.; Pust, D.

    1974-01-01

    Velocity distributions in molecular beams from free jets of light gases (He, H 2 and mixtures of 1% Xe in H 2 ) were studied as a function of the source Knudsen number. They were found to be narrower than what would be expected from previous studies. Mach numbers of 50 were observed for helium at a source temperature of T=85 deg K. The speed ratio for sources at room temperature was found to be S=29 for pure H 2 and 35 for a 1% Xe-99% H 2 mixture

  7. A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

    International Nuclear Information System (INIS)

    Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

    2008-01-01

    A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD 4 molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD 3 product. Preliminary results were also reported on the F+SiH 4 reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

  8. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  9. Chemical reaction dynamics using the Advanced Light Source

    International Nuclear Information System (INIS)

    Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.

    1995-01-01

    The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10(sup 16) photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source

  10. Chemical reaction dynamics using the Advanced Light Source

    International Nuclear Information System (INIS)

    Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.

    1995-09-01

    The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10 16 photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source

  11. Heat sources for bright-rimmed molecular clouds: CO observations of NGC 7822

    International Nuclear Information System (INIS)

    Elmegreen, B.G.; Dickinson, D.F.; Lada, C.J.

    1978-01-01

    Observations of the 2.6 mm carbon monoxide line in the bright rim NGC 7822 reveal that the peak excitation and column density of the molecule lie in a ridge ahead of the ionization front. Several possibilities for the excitation of this ridge are discussed. Cosmic rays are shown to provide an excellent heat source for Bok globules, but they can account for only approx.20% of the required heating in NGC 7822. Direct shock or compressional heating of the gas could be adequate only if the pressure inside the cloud is much larger than the thermal pressure. If, in fact, this internal pressure is determined by the source of line broadening (e.g., magnetic fields or turbulence), then shock or compressional heating could be important, and pressure equilibrium may exist between the neutral cloud and the bright rim. Heating by warm grains or by the photoelectric effect is also considered, but such mechanisms are probably not important if the only source of radiation is external to the cloud. This is primarily a result of the low cloud density (approx.10 3 cm -3 ) inferred from our observations. The extent to which unknown embedded stars may provide the required gaseous heating cannot be estimated from our observations of NGC 7822.An interesting and new heat source is suggested which may have important applications to bright-rimmed clouds or to any other predominantly neutral clouds that may have undergone some recent compression. We suggest that the heat input to neutral gas due to the relaxation of internal magnetic fields will be greatly enhanced during cloud compression (with or without a shock). We show that the power input to the gas will increase more with increasing density than will the cooling rate. As a result, cloud compression can lead to an increase in the gas temperature for a period lasting several million years, which is the decay time of the compressed field. The observed ridge in NGC 7822 may be due to stimulated release of internal magnetic energy

  12. Herschel observations of extraordinary sources: Analysis of the full Herschel/HIFI molecular line survey of sagittarius B2(N)

    Energy Technology Data Exchange (ETDEWEB)

    Neill, Justin L.; Bergin, Edwin A.; Crockett, Nathan R.; Favre, Cécile; Anderson, Dana E.; Burkhardt, Andrew M.; McNeill, Trevor D. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Lis, Dariusz C.; Emprechtinger, Martin; Monje, Raquel R.; Phillips, Thomas G. [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States); Schilke, Peter; Comito, Claudia; Qin, Sheng-Li [Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 Köln (Germany); Chen, Jo-Hsin [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Harris, Brent J.; Steber, Amanda L.; Vasyunina, Tatiana [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, VA 22904 (United States); Lord, Steven D. [National Herschel Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); McGuire, Brett A., E-mail: jneill@umich.edu, E-mail: ebergin@umich.edu [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States); and others

    2014-07-01

    A sensitive broadband molecular line survey of the Sagittarius B2(N) star-forming region has been obtained with the Heterodyne Instrument for the Far-Infrared (HIFI) instrument on the Herschel Space Observatory, offering the first high spectral resolution look at this well-studied source in a wavelength region largely inaccessible from the ground (625-157 μm). From the roughly 8000 spectral features in the survey, a total of 72 isotopologues arising from 44 different molecules have been identified, ranging from light hydrides to complex organics, and arising from a variety of environments from cold and diffuse to hot and dense gas. We present a local thermodynamic equilibrium (LTE) model to the spectral signatures of each molecule, constraining the source sizes for hot core species with complementary Submillimeter Array interferometric observations and assuming that molecules with related functional group composition are cospatial. For each molecule, a single model is given to fit all of the emission and absorption features of that species across the entire 480-1910 GHz spectral range, accounting for multiple temperature and velocity components when needed to describe the spectrum. As with other HIFI surveys toward massive star-forming regions, methanol is found to contribute more integrated line intensity to the spectrum than any other species. We discuss the molecular abundances derived for the hot core where the LTE approximation is generally found to describe the spectrum well, in comparison to abundances derived for the same molecules in the Orion KL region from a similar HIFI survey. Notably, we find significantly higher abundances of amine- and amide-bearing molecules (CH{sub 3}NH{sub 2}, CH{sub 2}NH, and NH{sub 2}CHO) toward Sgr B2(N) than Orion KL and lower abundances of some complex oxygen-bearing molecules (CH{sub 3}OCHO in particular). In addition to information on the chemical composition of the hot core, the strong far-infrared dust continuum allows

  13. Development of an electrically driven molecular motor.

    Science.gov (United States)

    Murphy, Colin J; Sykes, E Charles H

    2014-10-01

    For molecules to be used as components in molecular machinery, methods are required that couple individual molecules to external energy sources in order to selectively excite motion in a given direction. While significant progress has been made in the construction of synthetic molecular motors powered by light and by chemical reactions, there are few experimental examples of electrically driven molecular motors. To this end, we pioneered the use of a new, stable and tunable molecular rotor system based on surface-bound thioethers to comprehensively study many aspects of molecular rotation. As biological molecular motors often operate at interfaces, our synthetic system is especially amenable to microscopic interrogation as compared to solution-based systems. Using scanning tunneling microscopy (STM) and density functional theory, we studied the rotation of surface-bound thioethers, which can be induced either thermally or by electrons from the STM tip in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. This work culminated in the first experimental demonstration of a single-molecule electric motor, where the electrically driven rotation of a butyl methyl sulfide molecule adsorbed on a copper surface could be directionally biased. The direction and rate of the rotation are related to the chirality of both the molecule and the STM tip (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Infrared reflection nebulae in Orion Molecular Cloud

    International Nuclear Information System (INIS)

    Pendleton, Y.; Werner, M.W.; Capps, R.; Lester, D.; Hawaii Univ., Honolulu; Texas Univ., Austin)

    1986-01-01

    New observations of Orion Molecular Cloud 2 have been made from 1 to 100 microns using the NASA Infrared Telescope Facility and the Kuiper Airborne Observatory. An extensive program of polarimetry, photometry, and spectrophotometry has shown that the extended emission regions associated with two of the previously known near-infrared sources, IRS 1 and IRS 4, are infrared reflection nebulae, and that the compact sources IRS 1 and IRS 4 are the main luminosity sources in the cloud. The constraints from the far-infrared observations and an analysis of the scattered light from the IRS 1 nebula show that OMC-2/IRS 1 can be characterized by L of 500 solar luminosities or less and T of roughly 1000 K. The near-infrared albedo of the grains in the IRS 1 nebula is greater than 0.08. 27 references

  15. Radical-source molecular beam epitaxy of ZnO-based heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Sadofiev, Sergey

    2009-10-27

    This work focuses on the development of the novel growth approaches for the fabrication of Group II-oxide materials in the form of epitaxial films and heterostructures. It is shown that molecular-beam epitaxial growth far from thermal equilibrium allows one to overcome the standard solubility limit and to alloy ZnO with MgO or CdO in strict wurtzite phase up to mole fractions of several 10 %. In this way, a band-gap range from 2.2 to 4.4 eV can be covered. A clear layer-by-layer growth mode controlled by oscillations in reflection high-energy electron diffraction makes it possible to fabricate atomically smooth heterointerfaces and well-defined quantum well structures exhibiting prominent band-gap related light emission in the whole composition range. On appropriately designed structures, laser action from the ultraviolet down to green wavelengths and up to room temperature is achieved. The properties and potential of the ''state-of-the-art'' materials are discussed in relation to the advantages for their applications in various optoelectronic devices. (orig.)

  16. Low chromatic aberration hexapole for molecular state selection

    International Nuclear Information System (INIS)

    Ke, Yi; Deng, Xiao-Bing; Hu, Zhong-Kun

    2016-01-01

    In molecular beam state-selection experiments, the electrostatic hexapole acts as an optical lens, imaging molecules from the source to the focus. The molecular longitudinal velocity spread induces the phenomenon of chromatic aberration, which will reduce the state-selection purity. We propose a scheme which can effectively reduce the chromatic aberration by changing the hexapole voltage operating manner. The hexapole is already charged before molecules arrive at the entrance of the hexapole. When molecules are completely inside the hexapole, the voltage is switched off rapidly at an appropriate time. In this manner, faster molecules travel a longer hexapole focusing region than slower molecules. Therefore the focusing positions of molecules with different velocities become close. Numerical trajectory simulations of molecular state selection are carried out, and the results show that this low chromatic aberration hexapole can significantly improve the state purity from 46.2% to 87.0%. (paper)

  17. TAE+ 5.2 - TRANSPORTABLE APPLICATIONS ENVIRONMENT PLUS, VERSION 5.2 (DEC RISC ULTRIX VERSION)

    Science.gov (United States)

    TAE SUPPORT OFFICE

    1994-01-01

    TAE (Transportable Applications Environment) Plus is an integrated, portable environment for developing and running interactive window, text, and graphical object-based application systems. The program allows both programmers and non-programmers to easily construct their own custom application interface and to move that interface and application to different machine environments. TAE Plus makes both the application and the machine environment transparent, with noticeable improvements in the learning curve. The main components of TAE Plus are as follows: (1) the WorkBench, a What You See Is What You Get (WYSIWYG) tool for the design and layout of a user interface; (2) the Window Programming Tools Package (WPT), a set of callable subroutines that control an application's user interface; and (3) TAE Command Language (TCL), an easy-to-learn command language that provides an easy way to develop an executable application prototype with a run-time interpreted language. The WorkBench tool allows the application developer to interactively construct the layout of an application's display screen by manipulating a set of interaction objects including input items such as buttons, icons, and scrolling text lists. User interface interactive objects include data-driven graphical objects such as dials, thermometers, and strip charts as well as menubars, option menus, file selection items, message items, push buttons, and color loggers. The WorkBench user specifies the windows and interaction objects that will make up the user interface, then specifies the sequence of the user interface dialogue. The description of the designed user interface is then saved into resource files. For those who desire to develop the designed user interface into an operational application, the WorkBench tool also generates source code (C, C++, Ada, and TCL) which fully controls the application's user interface through function calls to the WPTs. The WPTs are the runtime services used by application

  18. phylo-node: A molecular phylogenetic toolkit using Node.js.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

  19. Improved Ambient Pressure Pyroelectric Ion Source

    Science.gov (United States)

    Beegle, Luther W.; Kim, Hugh I.; Kanik, Isik; Ryu, Ernest K.; Beckett, Brett

    2011-01-01

    The detection of volatile vapors of unknown species in a complex field environment is required in many different applications. Mass spectroscopic techniques require subsystems including an ionization unit and sample transport mechanism. All of these subsystems must have low mass, small volume, low power, and be rugged. A volatile molecular detector, an ambient pressure pyroelectric ion source (APPIS) that met these requirements, was recently reported by Caltech researchers to be used in in situ environments.

  20. Elasto-Plastic Behavior of Aluminum Foams Subjected to Compression Loading

    Science.gov (United States)

    Silva, H. M.; Carvalho, C. D.; Peixinho, N. R.

    2017-05-01

    The non-linear behavior of uniform-size cellular foams made of aluminum is investigated when subjected to compressive loads while comparing numerical results obtained in the Finite Element Method software (FEM) ANSYS workbench and ANSYS Mechanical APDL (ANSYS Parametric Design Language). The numerical model is built on AUTODESK INVENTOR, being imported into ANSYS and solved by the Newton-Raphson iterative method. The most similar conditions were used in ANSYS mechanical and ANSYS workbench, as possible. The obtained numerical results and the differences between the two programs are presented and discussed

  1. TURBULENCE DECAY AND CLOUD CORE RELAXATION IN MOLECULAR CLOUDS

    International Nuclear Information System (INIS)

    Gao, Yang; Law, Chung K.; Xu, Haitao

    2015-01-01

    The turbulent motion within molecular clouds is a key factor controlling star formation. Turbulence supports molecular cloud cores from evolving to gravitational collapse and hence sets a lower bound on the size of molecular cloud cores in which star formation can occur. On the other hand, without a continuous external energy source maintaining the turbulence, such as in molecular clouds, the turbulence decays with an energy dissipation time comparable to the dynamic timescale of clouds, which could change the size limits obtained from Jean's criterion by assuming constant turbulence intensities. Here we adopt scaling relations of physical variables in decaying turbulence to analyze its specific effects on the formation of stars. We find that the decay of turbulence provides an additional approach for Jeans' criterion to be achieved, after which gravitational infall governs the motion of the cloud core. This epoch of turbulence decay is defined as cloud core relaxation. The existence of cloud core relaxation provides a more complete understanding of the effect of the competition between turbulence and gravity on the dynamics of molecular cloud cores and star formation

  2. Argo: an integrative, interactive, text mining-based workbench supporting curation

    Science.gov (United States)

    Rak, Rafal; Rowley, Andrew; Black, William; Ananiadou, Sophia

    2012-01-01

    Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in

  3. A relationship between SNR G109.1-1.0 and the molecular cloud of Sh2-152

    International Nuclear Information System (INIS)

    Heydari-Malayeri, M.; Kahane, C.; Lucas, R.

    1981-01-01

    The possible association of the supernova remnant SNR G109.1 - 1.0 and the x-ray source GF2259 + 586 with the molecular cloud of Sh2 - 152 has been investigated by observing the molecular line 13 CO (J = 1 → 0) of the complex Sh2 - 147/Sh2 - 153. The present results are compared with those of previous workers. It is shown that although the various estimates of distance for the SNR, the x-ray source, the H II region Sh2 - 152 and the molecular cloud are in relatively good agreement, because of the uncertainties of distance evaluation in the Perseus arm this cannot be regarded as conclusive proof of the association of these objects. (U.K.)

  4. Metrological-grade tunable coherent source in the mid-infrared for molecular precision spectroscopy

    Science.gov (United States)

    Insero, G.; Clivati, C.; D'Ambrosio, D.; Cancio Pastor, P.; Verde, M.; Schunemann, P. G.; Zondy, J.-J.; Inguscio, M.; Calonico, D.; Levi, F.; De Natale, P.; Santambrogio, G.; Borri, S.

    2018-02-01

    We report on a metrological-grade mid-IR source with a 10-14 short-term instability for high-precision spectroscopy. Our source is based on the combination of a quantum cascade laser and a coherent radiation obtained by difference-frequency generation in an orientation-patterned gallium phosphide (OP-GaP) crystal. The pump and signal lasers are locked to an optical frequency comb referenced to the primary frequency standard via an optical fiber link. We demonstrate the robustness of the apparatus by measuring a vibrational transition around 6 μm on a metastable state of CO molecuels with 11 digits of precision.

  5. HERSCHEL MEASUREMENTS OF MOLECULAR OXYGEN IN ORION

    International Nuclear Information System (INIS)

    Goldsmith, Paul F.; Chen, Jo-Hsin; Li Di; Liseau, Rene; Black, John H.; Bell, Tom A.; Hollenbach, David; Kaufman, Michael J.; Lis, Dariusz C.; Melnick, Gary; Neufeld, David; Pagani, Laurent; Encrenaz, Pierre; Snell, Ronald; Benz, Arnold O.; Bruderer, Simon; Bergin, Edwin; Caselli, Paola; Caux, Emmanuel; Falgarone, Edith

    2011-01-01

    We report observations of three rotational transitions of molecular oxygen (O 2 ) in emission from the H 2 Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s -1 to 12 km s -1 and widths of 3 km s -1 . The beam-averaged column density is N(O 2 ) = 6.5 x 10 16 cm -2 , and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O 2 relative to H 2 is (0.3-7.3) x 10 -6 . The unusual velocity suggests an association with a ∼5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is ∼10 M sun and the dust temperature is ≥150 K. Our preferred explanation of the enhanced O 2 abundance is that dust grains in this region are sufficiently warm (T ≥ 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O 2 . For this small source, the line ratios require a temperature ≥180 K. The inferred O 2 column density ≅5 x 10 18 cm -2 can be produced in Peak A, having N(H 2 ) ≅ 4 x 10 24 cm -2 . An alternative mechanism is a low-velocity (10-15 km s -1 ) C-shock, which can produce N(O 2 ) up to 10 17 cm -2 .

  6. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    Energy Technology Data Exchange (ETDEWEB)

    Li, King C.P. [Department of Radiology, Methodist Hospital, Weill Cornell Medical College, 6565 Fannin Street, D280 Houston, TX 77030 (United States)], E-mail: kli@tmhs.org

    2009-05-15

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  7. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    International Nuclear Information System (INIS)

    Li, King C.P.

    2009-01-01

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  8. A molecular fragment cheminformatics roadmap for mesoscopic simulation.

    Science.gov (United States)

    Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

    2014-12-01

    Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and

  9. MILKY WAY STAR-FORMING COMPLEXES AND THE TURBULENT MOTION OF THE GALAXY'S MOLECULAR GAS

    International Nuclear Information System (INIS)

    Lee, Eve J.; Rahman, Mubdi; Murray, Norman

    2012-01-01

    We analyze Spitzer GLIMPSE, Midcourse Space Experiment (MSX), and Wilkinson Microwave Anisotropy Probe (WMAP) images of the Milky Way to identify 8 μm and free-free sources in the Galaxy. Seventy-two of the 88 WMAP sources have coverage in the GLIMPSE and MSX surveys suitable for identifying massive star-forming complexes (SFCs). We measure the ionizing luminosity functions of the SFCs and study their role in the turbulent motion of the Galaxy's molecular gas. We find a total Galactic free-free flux f ν = 46,177.6 Jy; the 72 WMAP sources with full 8 μm coverage account for 34,263.5 Jy (∼75%), with both measurements made at ν = 94 GHz (W band). We find a total of 280 SFCs, of which 168 have unique kinematic distances and free-free luminosities. We use a simple model for the radial distribution of star formation to estimate the free-free and ionizing luminosity for the sources lacking distance determinations. The total dust-corrected ionizing luminosity is Q = (2.9 ± 0.5) × 10 53 photons s –1 , which implies a Galactic star formation rate of M-dot * = 1.2±0.2 M ☉ yr -1 . We present the (ionizing) luminosity function of the SFCs and show that 24 sources emit half the ionizing luminosity of the Galaxy. The SFCs appear as bubbles in GLIMPSE or MSX images; the radial velocities associated with the bubble walls allow us to infer the expansion velocity of the bubbles. We calculate the kinetic luminosity of the bubble expansion and compare it to the turbulent luminosity of the inner molecular disk. SFCs emitting 80% of the total Galactic free-free luminosity produce a kinetic luminosity equal to 65% of the turbulent luminosity in the inner molecular disk. This suggests that the expansion of the bubbles is a major driver of the turbulent motion of the inner Milky Way molecular gas.

  10. Molecular hydrogen jets from the Orion nebula

    International Nuclear Information System (INIS)

    Taylor, K.N.R.; Storey, J.W.V.; Zealey, W.J.

    1984-01-01

    In an attempt to understand the relationship of the recently discovered complex of Herbig Haro objects in Orion to the IR sources in this region, the authors have carried out a survey of the molecular hydrogen S(1) line distribution. The observations have led to the discovery of a previously unsuspected structure of finger-like filaments of H 2 emission extending radially outwards from a common centre at IRC9. (author)

  11. Dzyaloshinskii-Moriya interactions and adiabatic magnetization dynamics in molecular magnets

    NARCIS (Netherlands)

    De Raedt, H; Miyashita, S; Michielsen, K; Machida, M

    A microscopic model of the molecular magnet V-15 is used to study mechanisms for the adiabatic change of the magnetization in time-dependent magnetic fields. The effects of the Dzyaloshinskii-Moriya interaction, the most plausible source for the energy-level repulsions that lead to adiabatic changes

  12. Microstructures of GaN1-xPx layers grown on (0001) GaN substrates by gas source molecular beam epitaxy

    Science.gov (United States)

    Seong, Tae-Yeon; Bae, In-Tae; Choi, Chel-Jong; Noh, D. Y.; Zhao, Y.; Tu, C. W.

    1999-03-01

    Transmission electron microscope (TEM), transmission electron diffraction (TED), and synchrotron x-ray diffraction (XRD) studies have been performed to investigate microstructural behavior of gas source molecular beam epitaxial GaN1-xPx layers grown on (0001) GaN/sapphire at temperatures (Tg) in the range 500-760 °C. TEM, TED, and XRD results indicate that the samples grown at Tg⩽600 °C undergo phase separation resulting in a mixture of GaN-rich and GaP-rich GaNP with zinc-blende structure. However, the samples grown at Tg⩾730 °C are found to be binary zinc-blende GaN(P) single crystalline materials. As for the 500 °C layer, the two phases are randomly oriented and distributed, whereas the 600 °C layer consists of phases that are elongated and inclined by 60°-70° clockwise from the [0001]α-GaN direction. The samples grown at Tg⩾730 °C are found to consist of two types of microdomains, namely, GaN(P)I and GaN(P)II; the former having twin relation to the latter.

  13. High-quality AlGaN/GaN grown on sapphire by gas-source molecular beam epitaxy using a thin low-temperature AlN layer

    Energy Technology Data Exchange (ETDEWEB)

    Jurkovic, M.J.; Li, L.K.; Turk, B.; Wang, W.I.; Syed, S.; Simonian, D.; Stormer, H.L.

    2000-07-01

    Growth of high-quality AlGaN/GaN heterostructures on sapphire by ammonia gas-source molecular beam epitaxy is reported. Incorporation of a thin AlN layer grown at low temperature within the GaN buffer is shown to result in enhanced electrical and structural characteristics for subsequently grown heterostructures. AlGaN/GaN structures exhibiting reduced background doping and enhanced Hall mobilities (2100, 10310 and 12200 cm{sup 2}/Vs with carrier sheet densities of 6.1 x 10{sup 12} cm{sup {minus}2}, and 5.8 x 10{sup 12} cm{sup {minus}2} at 300 K, 77 K, and 0.3 K, respectively) correlate with dislocation filtering in the thin AlN layer. Magnetotransport measurements at 0.3 K reveal well-resolved Shubnikov-de Haas oscillations starting at 3 T.

  14. Molecular beam (1-50eV) production by duoplasmatron source

    International Nuclear Information System (INIS)

    Delmas, M.; Gautherin, G.; Lejeune, C.

    1974-01-01

    The duoplasmatron discharge is commonly used to produce intense ion beams. A theoretical model of this discharge has been previously developed. The analysis of charge exchange processes between ions and neutral within the discharge shows that the source is able to deliver intense neutral beams (10 16 part s -1 ), the energy being in the range 1-50 eV. The intensity and energy distribution may be controlled from the discharge parameter variations. An experimental device has been realized in order to separate the neutral beam and the flux of charged particles; these latter are injected axially in a toroidal magnetic field configuration [fr

  15. Gesture Interaction Browser-Based 3D Molecular Viewer.

    Science.gov (United States)

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

  16. Molecular Epidemiology of Group A Rotaviruses in Water Sources and Selected Raw Vegetables in Southern Africa

    Science.gov (United States)

    van Zyl, W. B.; Page, N. A.; Grabow, W. O. K.; Steele, A. D.; Taylor, M. B.

    2006-01-01

    Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development. PMID:16820443

  17. MOLECULAR EVALUATION OF CHANGES IN PLANKTONIC BACTERIAL POPULATIONS RESULTING FROM EQUINE FECAL CONTAMINATION IN A SUB-WATERSHED

    Science.gov (United States)

    Considerable emphasis has been placed on developing watershed-based strategies with the potential to reduce non-point-source fecal contamination. Molecular methods applied used 16S-ribosomal-deoxyribonucleic-acid (rDNA) to try to determine sources of fecal contamination. Objectiv...

  18. Special issue on compact x-ray sources

    Science.gov (United States)

    Hooker, Simon; Midorikawa, Katsumi; Rosenzweig, James

    2014-04-01

    Journal of Physics B: Atomic, Molecular and Optical Physics is delighted to announce a forthcoming special issue on compact x-ray sources, to appear in the winter of 2014, and invites you to submit a paper. The potential for high-brilliance x- and gamma-ray sources driven by advanced, compact accelerators has gained increasing attention in recent years. These novel sources—sometimes dubbed 'fifth generation sources'—will build on the revolutionary advance of the x-ray free-electron laser (FEL). New radiation sources of this type have widespread applications, including in ultra-fast imaging, diagnostic and therapeutic medicine, and studies of matter under extreme conditions. Rapid advances in compact accelerators and in FEL techniques make this an opportune moment to consider the opportunities which could be realized by bringing these two fields together. Further, the successful development of compact radiation sources driven by compact accelerators will be a significant milestone on the road to the development of high-gradient colliders able to operate at the frontiers of particle physics. Thus the time is right to publish a peer-reviewed collection of contributions concerning the state-of-the-art in: advanced and novel acceleration techniques; sophisticated physics at the frontier of FELs; and the underlying and enabling techniques of high brightness electron beam physics. Interdisciplinary research connecting two or more of these fields is also increasingly represented, as exemplified by entirely new concepts such as plasma based electron beam sources, and coherent imaging with fs-class electron beams. We hope that in producing this special edition of Journal of Physics B: Atomic, Molecular and Optical Physics (iopscience.iop.org/0953-4075/) we may help further a challenging mission and ongoing intellectual adventure: the harnessing of newly emergent, compact advanced accelerators to the creation of new, agile light sources with unprecedented capabilities

  19. Molmil: a molecular viewer for the PDB and beyond.

    Science.gov (United States)

    Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

    2016-01-01

    We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

  20. Molecular sensors and molecular logic gates

    International Nuclear Information System (INIS)

    Georgiev, N.; Bojinov, V.

    2013-01-01

    Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

  1. A blind green bank telescope millimeter-wave survey for redshifted molecular absorption

    Energy Technology Data Exchange (ETDEWEB)

    Kanekar, N.; Gupta, A. [National Centre for Radio Astrophysics, TIFR, Ganeshkhind, Pune 411007 (India); Carilli, C. L. [National Radio Astronomy Observatory, 1003 Lopezville Road, Socorro, NM 87801 (United States); Stocke, J. T. [CASA, Department of Astrophysical and Planetary Sciences, University of Colorado, 389-UCB, Boulder, CO 80309 (United States); Willett, K. W., E-mail: nkanekar@ncra.tifr.res.in [School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455 (United States)

    2014-02-10

    We present the methodology for 'blind' millimeter-wave surveys for redshifted molecular absorption in the CO/HCO{sup +} rotational lines. The frequency range 30-50 GHz appears optimal for such surveys, providing sensitivity to absorbers at z ≳ 0.85. It is critical that the survey is 'blind', i.e., based on a radio-selected sample, including sources without known redshifts. We also report results from the first large survey of this kind, using the Q-band receiver on the Green Bank Telescope (GBT) to search for molecular absorption toward 36 sources, 3 without known redshifts, over the frequency range 39.6-49.5 GHz. The GBT survey has a total redshift path of Δz ≈ 24, mostly at 0.81 < z < 1.91, and a sensitivity sufficient to detect equivalent H{sub 2} column densities ≳ 3 × 10{sup 21} cm{sup –2} in absorption at 5σ significance (using CO-to-H{sub 2} and HCO{sup +}-to-H{sub 2} conversion factors of the Milky Way). The survey yielded no confirmed detections of molecular absorption, yielding the 2σ upper limit n(z = 1.2) < 0.15 on the redshift number density of molecular gas at column densities N(H{sub 2}) ≳ 3 × 10{sup 21} cm{sup –2}.

  2. Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water.

    Science.gov (United States)

    Ahmed, W; Staley, C; Sadowsky, M J; Gyawali, P; Sidhu, J P S; Palmer, A; Beale, D J; Toze, S

    2015-10-01

    In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. Copyright © 2015, American Society for Microbiology

  3. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huber, Charles S. [Instituto Federal Sul-rio-grandense, Câmpus Pelotas, Pelotas, RS (Brazil); Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Universidade Federal de Santa Catarina, Departamento de Química, Florianópolis, SC (Brazil); Andrade, Jailson B. [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg{sup −1} and 4.7 mg kg{sup −1}, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol.

  4. Free and Open Source Chemistry Software in Research of Quantitative Structure-Toxicity Relationship of Pesticides

    Directory of Open Access Journals (Sweden)

    Rastija Vesna

    2017-01-01

    Full Text Available Pesticides are toxic chemicals aimed for the destroying pest on crops. Numerous data evidence about toxicity of pesticides on aquatic organisms. Since pesticides with similar properties tend to have similar biological activities, toxicity may be predicted from structure. Their structure feature and properties are encoded my means of molecular descriptors. Molecular descriptors can capture quite simple two-dimensional (2D chemical structures to highly complex three-dimensional (3D chemical structures. Quantitative structure-toxicity relationship (QSTR method uses linear regression analyses for correlation toxicity of chemical with their structural feature using molecular descriptors. Molecular descriptors were calculated using open source software PaDEL and in-house built PyMOL plugin (PyDescriptor. PyDescriptor is a new script implemented with the commonly used visualization software PyMOL for calculation of a large and diverse set of easily interpretable molecular descriptors encoding pharmacophoric patterns and atomic fragments. PyDescriptor has several advantages like free and open source, can work on all major platforms (Windows, Linux, MacOS. QSTR method allows prediction of toxicity of pesticides without experimental assay. In the present work, QSTR analysis for toxicity of a dataset of mixtures of 5 classes of pesticides comprising has been performed.

  5. GRASS GIS: The first Open Source Temporal GIS

    Science.gov (United States)

    Gebbert, Sören; Leppelt, Thomas

    2015-04-01

    over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

  6. The Denver Aerosol Sources and Health (DASH) study: Overview and early findings

    Science.gov (United States)

    Vedal, S.; Hannigan, M. P.; Dutton, S. J.; Miller, S. L.; Milford, J. B.; Rabinovitch, N.; Kim, S.-Y.; Sheppard, L.

    Improved understanding of the sources of air pollution that are most harmful could aid in developing more effective measures for protecting human health. The Denver Aerosol Sources and Health (DASH) study was designed to identify the sources of ambient fine particulate matter (PM 2.5) that are most responsible for the adverse health effects of short-term exposure to PM 2.5. Daily 24-h PM 2.5 sampling began in July 2002 at a residential monitoring site in Denver, Colorado, using both Teflon and quartz filter samplers. Sampling is planned to continue through 2008. Chemical speciation is being carried out for mass, inorganic ionic compounds (sulfate, nitrate and ammonium), and carbonaceous components, including elemental carbon, organic carbon, temperature-resolved organic carbon fractions and a large array of organic compounds. In addition, water-soluble metals were measured daily for 12 months in 2003. A receptor-based source apportionment approach utilizing positive matrix factorization (PMF) will be used to identify PM 2.5 source contributions for each 24-h period. Based on a preliminary assessment using synthetic data, the proposed source apportionment should be able to identify many important sources on a daily basis, including secondary ammonium nitrate and ammonium sulfate, diesel vehicle exhaust, road dust, wood combustion and vegetative debris. Meat cooking, gasoline vehicle exhaust and natural gas combustion were more challenging for PMF to accurately identify due to high detection limits for certain organic molecular marker compounds. Measurements of these compounds are being improved and supplemented with additional organic molecular marker compounds. The health study will investigate associations between daily source contributions and an array of health endpoints, including daily mortality and hospitalizations and measures of asthma control in asthmatic children. Findings from the DASH study, in addition to being of interest to policymakers, by

  7. Molecular absorption spectrometry in flames and furnaces: A review

    Energy Technology Data Exchange (ETDEWEB)

    Butcher, David J., E-mail: butcher@email.wcu.edu

    2013-12-04

    Graphical abstract: -- Highlights: •Theory and analytical considerations for molecular absorption spectrometry (MAS). •Critical review of low resolution MAS. •Critical review of the analytical performance of high-resolution continuum source (HR-CS) flame MAS. •Critical review of the analytical performance of HR-CS graphite furnace MAS. •Current status of HR-CS MAS and its future prospects for elemental analysis. -- Abstract: Molecular absorption spectrometry (MAS), originally developed in the 1970s, is a technique to determine non-metals in flames and graphite furnaces by monitoring the absorbance of diatomic molecules. Early studies employed low resolution instruments designed for line source atomic absorption, which provided a limited choice of analytical wavelengths, insufficient spectral resolution, and spectral interferences. However, the development of high-resolution continuum source atomic absorption spectrometry (HR-CS AAS) instrumentation has allowed the analysis of challenging samples for non-metals as well as some difficult elements to determine by AAS, such as aluminum and phosphorus. In this review, theory and analytical considerations for MAS are discussed. The principles and limitations of low resolution MAS are described, along with its applications. HR-CS AAS instrumentation is reviewed, emphasizing performance characteristics most relevant for MAS. Applications of flame and HR-CS GFMAS are reviewed, highlighting the most significant work to date. The paper concludes with an evaluation of the enhanced analytical capabilities provided by HR-CS MAS.

  8. Artificial muscle-like function from hierarchical supramolecular assembly of photoresponsive molecular motors.

    Science.gov (United States)

    Chen, Jiawen; Leung, Franco King-Chi; Stuart, Marc C A; Kajitani, Takashi; Fukushima, Takanori; van der Giessen, Erik; Feringa, Ben L

    2018-02-01

    A striking feature of living systems is their ability to produce motility by amplification of collective molecular motion from the nanoscale up to macroscopic dimensions. Some of nature's protein motors, such as myosin in muscle tissue, consist of a hierarchical supramolecular assembly of very large proteins, in which mechanical stress induces a coordinated movement. However, artificial molecular muscles have often relied on covalent polymer-based actuators. Here, we describe the macroscopic contractile muscle-like motion of a supramolecular system (comprising 95% water) formed by the hierarchical self-assembly of a photoresponsive amphiphilic molecular motor. The molecular motor first assembles into nanofibres, which further assemble into aligned bundles that make up centimetre-long strings. Irradiation induces rotary motion of the molecular motors, and propagation and accumulation of this motion lead to contraction of the fibres towards the light source. This system supports large-amplitude motion, fast response, precise control over shape, as well as weight-lifting experiments in water and air.

  9. Artificial muscle-like function from hierarchical supramolecular assembly of photoresponsive molecular motors

    Science.gov (United States)

    Chen, Jiawen; Leung, Franco King-Chi; Stuart, Marc C. A.; Kajitani, Takashi; Fukushima, Takanori; van der Giessen, Erik; Feringa, Ben L.

    2018-02-01

    A striking feature of living systems is their ability to produce motility by amplification of collective molecular motion from the nanoscale up to macroscopic dimensions. Some of nature's protein motors, such as myosin in muscle tissue, consist of a hierarchical supramolecular assembly of very large proteins, in which mechanical stress induces a coordinated movement. However, artificial molecular muscles have often relied on covalent polymer-based actuators. Here, we describe the macroscopic contractile muscle-like motion of a supramolecular system (comprising 95% water) formed by the hierarchical self-assembly of a photoresponsive amphiphilic molecular motor. The molecular motor first assembles into nanofibres, which further assemble into aligned bundles that make up centimetre-long strings. Irradiation induces rotary motion of the molecular motors, and propagation and accumulation of this motion lead to contraction of the fibres towards the light source. This system supports large-amplitude motion, fast response, precise control over shape, as well as weight-lifting experiments in water and air.

  10. Radiation polymerization of acrylamide with super-high molecular weight in inverse emulsion

    International Nuclear Information System (INIS)

    Ye Qiang; Ge Xuewu; Xu Xiangling; Zhang Zhicheng

    1998-01-01

    The inverse emulsion polymerization of acrylamide has been studied with γ-ray initiation. Polyacrylamide with super high molecular weight over ten million (11 x 10 6 ), which is very important in application as flocculant, is obtained. In this work, some methods are taken to enhance the molecular weight as follows: (1) In order to prepare soluble polyacrylamide with super high molecular weight, the better conditions are: the emulsifier content is about 2% and the monomer concentration is about 20%∼24% in the composition of monomer emulsion, and the absorbed dose is about 500∼600 Gy. (2) Initiating with high dose rate and polymerizing with low dose rate can not only enhance the molecular weight of product, but also curtail the polymerizing time. (3) Stopping radiation when the conversion gets to about 10% and post-polymerizing outside the radiation source until the conversion gets to 82% can obtain polyacrylamide with super high molecular weight, and shorten the irradiation time as well

  11. Compact continuum radio sources in the Orion Nebula

    International Nuclear Information System (INIS)

    Garay, G.; Moran, J.M.; Reid, M.J.; European Southern Observatory, Garching, West Germany)

    1987-01-01

    The Orion Nebula was observed with the VLA in order to search for radio emission from compact H II regions indicative of embedded OB stars or from winds associated with pre-main sequence, low-mass stars. Fourteen of the 21 detected radio sources are within 30 arcsec of Omega 1 Orionis C; 13 of these objects are probably neutral condensations surrounded by ionized envelopes that are excited by the star. If the temperature of the ionized envelopes is 10,000 K and their electron densities decrease as the square of the distance from the core center, then a typical neutral condensation has a radius of 10 to the 15th cm and a peak electron density of 400,000/cu cm. Seven sources are in or near the Orion molecular cloud. Four of the sources have optical counterparts. Two are highly variable radio sources associated with X-ray sources, and two have radio spectra indicative of thermal emission. Two of the three optically invisible sources have radio emission likely to arise in a dense ionized envelope surrounding and excited by an early B-type star. 46 references

  12. MULTIPLE FAST MOLECULAR OUTFLOWS IN THE PRE-PLANETARY NEBULA CRL 618

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chin-Fei; Huang, Po-Sheng [Academia Sinica Institute of Astronomy and Astrophysics, P.O. Box 23-141, Taipei 106, Taiwan (China); Sahai, Raghvendra [Jet Propulsion Laboratory, MS 183-900, California Institute of Technology, Pasadena, CA 91109 (United States); Sánchez Contreras, Carmen [Astrobiology Center (CSIC-INTA), ESAC Campus, E-28691 Villanueva de la Canada, Madrid (Spain); Tay, Jeremy Jian Hao [Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore)

    2013-11-01

    CRL 618 is a well-studied pre-planetary nebula. It has multiple highly collimated optical lobes, fast molecular outflows along the optical lobes, and an extended molecular envelope that consists of a dense torus in the equator and a tenuous round halo. Here we present our observations of this source in CO J = 3-2 and HCN J = 4-3 obtained with the Submillimeter Array at up to ∼0.''3 resolutions. We spatially resolve the fast molecular outflow region previously detected in CO near the central star and find it to be composed of multiple outflows that have similar dynamical ages and are oriented along the different optical lobes. We also detect fast molecular outflows further away from the central star near the tips of the extended optical lobes and a pair of equatorial outflows inside the dense torus. We find that two episodes of bullet ejections in different directions are needed, one producing the fast molecular outflows near the central star and one producing the fast molecular outflows near the tips of the extended optical lobes. One possibility to launch these bullets is a magneto-rotational explosion of the stellar envelope.

  13. Background gas density and beam losses in NIO1 beam source

    Energy Technology Data Exchange (ETDEWEB)

    Sartori, E., E-mail: emanuele.sartori@igi.cnr.it; Veltri, P.; Serianni, G. [Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA), C.so Stati Uniti 4, 35127 Padova (Italy); Cavenago, M. [INFN-LNL, v.le dell’Università 2, I-35020 Legnaro (PD) (Italy)

    2016-02-15

    NIO1 (Negative Ion Optimization 1) is a versatile ion source designed to study the physics of production and acceleration of H- beams up to 60 keV. In ion sources, the gas is steadily injected in the plasma source to sustain the discharge, while high vacuum is maintained by a dedicated pumping system located in the vessel. In this paper, the three dimensional gas flow in NIO1 is studied in the molecular flow regime by the Avocado code. The analysis of the gas density profile along the accelerator considers the influence of effective gas temperature in the source, of the gas temperature accommodation by collisions at walls, and of the gas particle mass. The calculated source and vessel pressures are compared with experimental measurements in NIO1 during steady gas injection.

  14. Cellular and molecular interaction in HIV infection: A review | Timbo ...

    African Journals Online (AJOL)

    Objective: To review the cellular and molecular interactions between HIV and the host immune system that lead to full-blown AIDS. Data Sources: Published reports on HIV/host interaction during a fifteen year period beginning from 1987. Study selection: Only those studies involving humans and non-human primates were ...

  15. Plasma diagnostic tools for optimizing negative hydrogen ion sources

    International Nuclear Information System (INIS)

    Fantz, U.; Falter, H.D.; Franzen, P.; Speth, E.; Hemsworth, R.; Boilson, D.; Krylov, A.

    2006-01-01

    The powerful diagnostic tool of optical emission spectroscopy is used to measure the plasma parameters in negative hydrogen ion sources based on the surface mechanism. Results for electron temperature, electron density, atomic-to-molecular hydrogen density ratio, and gas temperature are presented for two types of sources, a rf source and an arc source, which are currently under development for a neutral beam heating system of ITER. The amount of cesium in the plasma volume is obtained from cesium radiation: the Cs neutral density is five to ten orders of magnitude lower than the hydrogen density and the Cs ion density is two to three orders of magnitude lower than the electron density in front of the grid. It is shown that monitoring of cesium lines is very useful for monitoring the cesium balance in the source. From a line-ratio method negative ion densities are determined. In a well-conditioned source the negative ion density is of the same order of magnitude as the electron density and correlates with extracted current densities

  16. Nanojets, Electrospray, and Ion Field Evaporation: Molecular Dynamics Simulations and Laboratory Experiments

    National Research Council Canada - National Science Library

    Luedtke, W. D; Landman, Uzi; Chiu, Y. H; Levandier, D. J; Dressler, R. A; Sok, S; Gordon, M. S

    2008-01-01

    ... experiment and using molecular dynamics (MD) simulations. The electrospray source is operated in a Taylor cone-jet mode, with the nanojet that forms being characterized by high surface-normal electric field strengths in the vicinity of I V/nm...

  17. High-efficiency silicon doping of InP and In0.53Ga0.47As in gas source and metalorganic molecular beam epitaxy using silicon tetrabromide

    International Nuclear Information System (INIS)

    Jackson, S.L.; Fresina, M.T.; Baker, J.E.; Stillman, G.E.

    1994-01-01

    Efficient vapor source Si doping of InP and In 0.53 Ga 0.47 As have been demonstrated using SiBr 4 as the Si source for both gas source (GSMBE) and metalorganic molecular beam epitaxy (MOMBE). Net electron concentrations ranging from n=2x10 17 to 6.8x10 19 cm -3 and from 9x10 16 to 3x10 19 cm -3 have been obtained for InP and In 0.53 Ga 0.47 As, respectively. Comparison of these data with those for Si 2 H 6 indicate that the Si incorporation efficiency with SiBr 4 is more than 10 000 times greater than with Si 2 H 6 for substrate temperatures in the range of 475≤T s ≤500 degree C. Specular surface morphologies were obtained, even for the most heavily doped samples. While [Si] as high as 1.8x10 20 cm -3 was obtained in InP, the net electron concentrations and 300 K Hall mobilities decrease with increasing [Si] for [Si]>6.8x10 19 cm -3 . Contact resistances as low as R c =3x10 -8 Ω cm 2 were obtained using a nonalloyed Ti/Pt/Au contact to InP layers doped to n=6.3x10 19 cm -3 . During GSMBE growth, an increased Si background concentration ([Si]∼2x10 17 cm -3 ) was observed after extended use of the SiBr 4 source for these heavy doping concentrations. This increased background was not observed in MOMBE-grown material. Depth profiles of pulse-doped structures indicate the absence of memory effects for structures grown by MOMBE

  18. Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist?

    Science.gov (United States)

    Fassan, Matteo

    2018-03-01

    - Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings. - To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice. - Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed. - Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed-material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.

  19. Biopython: freely available Python tools for computational molecular biology and bioinformatics

    DEFF Research Database (Denmark)

    Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T

    2009-01-01

    SUMMARY: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments......, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. AVAILABILITY: Biopython is freely available, with documentation and source code at (www...

  20. Microjet burners for molecular-beam sources and combustion studies

    Science.gov (United States)

    Groeger, Wolfgang; Fenn, John B.

    1988-09-01

    A novel microjet burner is described in which combustion is stabilized by a hot wall. The scale is so small that the entire burner flow can be passed through a nozzle only 0.2 mm or less in diameter into an evacuated chamber to form a supersonic free jet with expansion so rapid that all collisional processes in the jet gas are frozen in a microsecond or less. This burner can be used to provide high-temperature source gas for free jet expansion to produce intense beams of internally hot molecules. A more immediate use would seem to be in the analysis of combustion products and perhaps intermediates by various kinds of spectroscopies without some of the perturbation effects encountered in probe sampling of flames and other types of combustion devices. As an example of the latter application of this new tool, we present infrared emission spectra for jet gas obtained from the combustion of oxygen-hydrocarbon mixtures both fuel-rich and fuel-lean operation. In addition, we show results obtained by mass spectrometric analysis of the combustion products.

  1. National synchrotron light source. [Annual report], October 1, 1992--September 30, 1993

    International Nuclear Information System (INIS)

    Rothman, E.Z.; Hulbert, S.L.; Lazarz, N.M.

    1994-04-01

    This report contains brief discussions on the research being conducted at the National Synchrotron Light source. Some of the topics covered are: X-ray spectroscopy; nuclear physics; atomic and molecular science; meetings and workshops; operations; and facility improvements

  2. National synchrotron light source. [Annual report], October 1, 1992--September 30, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Rothman, E.Z.; Hulbert, S.L.; Lazarz, N.M. [eds.

    1994-04-01

    This report contains brief discussions on the research being conducted at the National Synchrotron Light source. Some of the topics covered are: X-ray spectroscopy; nuclear physics; atomic and molecular science; meetings and workshops; operations; and facility improvements.

  3. Report of the workshop on accelerator-based atomic and molecular science

    International Nuclear Information System (INIS)

    Meyerhof, W.E.

    1981-01-01

    This Workshop, held in New London, NH on July 27-30, 1980, had a registration of 43, representing an estimated one-third of all principal investigators in the United States in this research subfield. The workshop was organized into 5 working groups for the purpose of (1) identifying some vital physics problems which experimental and theoretical atomic and molecular science can address with current and projected techniques; (2) establishing facilities and equipment needs required to realize solutions to these problems; (3) formulating suggestions for a coherent national policy concerning this discipline; (4) assessing and projecting the manpower situation; and (5) evaluating the relations of this interdisciplinary science to other fields. Recommedations deal with equipment and operating costs for small accelerator laboratories, especially at universities; instrumentation of ion beam lines dedicated to atomic and molecular science at some large accelerators; development of low-velocity, high charge-state ion sources; synchrotron light sources; improvement or replacement of tandem van de Graaff accelerators; high-energy beam lines for atomic physics; the needs for postdoctoral support in this subfield; new accelerator development; need for representatives from atomic and molecular science on program committees for large national accelerator facilities; and the contributions the field can make to applied physics problems

  4. On-chip dual comb source for spectroscopy

    OpenAIRE

    Dutt, Avik; Joshi, Chaitanya; Ji, Xingchen; Cardenas, Jaime; Okawachi, Yoshitomo; Luke, Kevin; Gaeta, Alexander L.; Lipson, Michal

    2016-01-01

    Dual-comb spectroscopy is a powerful technique for real-time, broadband optical sampling of molecular spectra which requires no moving components. Recent developments with microresonator-based platforms have enabled frequency combs at the chip scale. However, the need to precisely match the resonance wavelengths of distinct high-quality-factor microcavities has hindered the development of an on-chip dual comb source. Here, we report the first simultaneous generation of two microresonator comb...

  5. Prediction With Dimension Reduction of Multiple Molecular Data Sources for Patient Survival

    Directory of Open Access Journals (Sweden)

    Adam Kaplan

    2017-07-01

    Full Text Available Predictive modeling from high-dimensional genomic data is often preceded by a dimension reduction step, such as principal component analysis (PCA. However, the application of PCA is not straightforward for multisource data, wherein multiple sources of ‘omics data measure different but related biological components. In this article, we use recent advances in the dimension reduction of multisource data for predictive modeling. In particular, we apply exploratory results from Joint and Individual Variation Explained (JIVE, an extension of PCA for multisource data, for prediction of differing response types. We conduct illustrative simulations to illustrate the practical advantages and interpretability of our approach. As an application example, we consider predicting survival for patients with glioblastoma multiforme from 3 data sources measuring messenger RNA expression, microRNA expression, and DNA methylation. We also introduce a method to estimate JIVE scores for new samples that were not used in the initial dimension reduction and study its theoretical properties; this method is implemented in the R package R.JIVE on CRAN, in the function jive.predict.

  6. Ultrafast molecular dynamics illuminated with synchrotron radiation

    International Nuclear Information System (INIS)

    Bozek, John D.; Miron, Catalin

    2015-01-01

    Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

  7. New trends in atomic and molecular physics advanced technological applications

    CERN Document Server

    2013-01-01

    The field of Atomic and Molecular Physics (AMP) has reached significant advances in high–precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy , astrophysics , fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) To...

  8. Ozonation of humic substances: Effects on molecular weight distributions of organic carbon and trihalomethane formation potential

    International Nuclear Information System (INIS)

    Amy, G.L.; Kuo, C.J.; Sierka, R.A.

    1988-01-01

    Four different sources of humic substances were studied to determine the effects of ozonation on molecular weight distributions, based on dissolved organic carbon (DOC) and trihalomethane formation potential (THMFP). Solutions of two soil-derived fulvic acids and a one soil-derived humic acid, as well as dissolved organic matter (DOM) associated with a natural water source were studied. Both gel permeation chromatography (GPC) and ultrafiltration (UF) were employed to define apparent molecular weight (AMW). Applied ozone doses ranged from 2.0 to 2.5 mg O 3 /mg DOC. Overall samples of untreated and ozonated waters, as well as individual molecular weight fractions, were characterized according to DOC, uv absorbance, and THMFP. Ozonation resulted in a significant disappearance of higher AMW material with a corresponding increase in lower AMW material. Although little overall reduction in DOC concentration was observed, significant overall reductions in UV absorbance and THMFP levels were observed

  9. Molecular Epidemiology of Plasmodium falciparum Malaria Outbreak, Tumbes, Peru, 2010-2012.

    Science.gov (United States)

    Baldeviano, G Christian; Okoth, Sheila Akinyi; Arrospide, Nancy; Gonzalez, Rommell V; Sánchez, Juan F; Macedo, Silvia; Conde, Silvia; Tapia, L Lorena; Salas, Carola; Gamboa, Dionicia; Herrera, Yeni; Edgel, Kimberly A; Udhayakumar, Venkatachalam; Lescano, Andrés G

    2015-05-01

    During 2010-2012, an outbreak of 210 cases of malaria occurred in Tumbes, in the northern coast of Peru, where no Plasmodium falciparum malaria case had been reported since 2006. To identify the source of the parasite causing this outbreak, we conducted a molecular epidemiology investigation. Microsatellite typing showed an identical genotype in all 54 available isolates. This genotype was also identical to that of parasites isolated in 2010 in the Loreto region of the Peruvian Amazon and closely related to clonet B, a parasite lineage previously reported in the Amazon during 1998-2000. These findings are consistent with travel history of index case-patients. DNA sequencing revealed mutations in the Pfdhfr, Pfdhps, Pfcrt, and Pfmdr1 loci, which are strongly associated with resistance to chloroquine and sulfadoxine/pyrimethamine, and deletion of the Pfhrp2 gene. These results highlight the need for timely molecular epidemiology investigations to trace the parasite source during malaria reintroduction events.

  10. Carbon source in the future chemical industries

    Science.gov (United States)

    Hofmann, Peter; Heinrich Krauch, Carl

    1982-11-01

    Rising crude oil prices favour the exploitation of hitherto unutilised energy carriers and the realisation of new technologies in all sectors where carbon is used. These changed economic constraints necessitate both savings in conventional petrochemistry and a change to oil-independent carbon sources in the chemical industry. While, in coal chemistry, the synthesis and process principles of petrochemistry — fragmentation of the raw material and subsequent buildup of molecular structures — can be maintained, the raw material structure largely remains unchanged in the chemistry of renewable raw materials. This lecture is to demonstrate the structural as well as the technological and energy criteria of the chemistry of alternative carbon sources, to forecast the chances of commercial realization and to discuss some promising fields of research and development.

  11. Modelling, Design, Growth and Characterization of Strain Balanced Quantum Cascade Lasers (3-11mum), grown by Gas Source Molecular Beam Epitaxy

    Science.gov (United States)

    Bandyopadhyay, Neelanjan

    Quantum Cascade Laser (QCL) is a compact room temperature (RT) source of mid-infrared radiation, which can be used for spectroscopic detection of trace amount of chemicals. The mid-infrared spectral range between (3-11 microm), has a dense array of absorption lines of numerous molecules, due to the presence of fundamental vibrational modes. The goal of this thesis can be subdivided into two parts. Firstly, short wavelength QCLs, emitting below 4microm, perform poorly at RT, due to inter-valley Gamma --- L carrier scattering, carrier escape to the continuum, heat removal from the core region at high power density corresponding to short wavelength operation, and large interface scattering due to highly strained materials. Secondly, it is desirable to have a single QCL based source emitting between 6-10microm, which be used to detect multiple molecules having their peak absorptions far apart, inside this spectral range. However, gain bandwidth of a single core QCL is relatively small, so laser emission cannot be tuned over a wide spectral range. This thesis describes the working principle of a QCL based on superlattice transport, rate equations, scattering mechanism, and waveguide design. The choice of the material system for this work and the fundamentals of band structure engineering has been derived. Gas source molecular beam epitaxy - growth optimization and characterization is one of the most important features of this work, especially for short wavelength QCLs, and has been explained in depth. Different strategies for design of active region design of short wavelength QCL and heterogeneous broadband QCL has been explored. The major milestones, of this research was the world's first watt level continuous wave (CW), RT demonstration at 3.76 microm, which was followed by another milestone of the first CW, RT demonstration at 3.39microm and 3.55microm, and finally the elusive result of QCL emitting at CW, RT at a wavelength as short as lambda ~3microm, a record. In

  12. Trimethylsilyl derivatives of organic compounds in source samples and in atmospheric fine particulate matter.

    Science.gov (United States)

    Nolte, Christopher G; Schauer, James J; Cass, Glen R; Simoneit, Bernd R T

    2002-10-15

    Source sample extracts of vegetative detritus, motor vehicle exhaust, tire dust paved road dust, and cigarette smoke have been silylated and analyzed by GC-MS to identify polar organic compounds that may serve as tracers for those specific emission sources of atmospheric fine particulate matter. Candidate molecular tracers were also identified in atmospheric fine particle samples collected in the San Joaquin Valley of California. A series of normal primary alkanols, dominated by even carbon-numbered homologues from C26 to C32, the secondary alcohol 10-nonacosanol, and some phytosterols are prominent polar compounds in the vegetative detritus source sample. No new polar organic compounds are found in the motor vehicle exhaust samples. Several hydrogenated resin acids are present in the tire dust sample, which might serve as useful tracers for those sources in areas that are heavily impacted by motor vehicle traffic. Finally, the alcohol and sterol emission profiles developed for all the source samples examined in this project are scaled according to the ambient fine particle mass concentrations attributed to those sources by a chemical mass balance receptor model that was previously applied to the San Joaquin Valley to compute the predicted atmospheric concentrations of individual alcohols and sterols. The resulting underprediction of alkanol concentrations at the urban sites suggests that alkanols may be more sensitive tracers for natural background from vegetative emissions (i.e., waxes) than the high molecular weight alkanes, which have been the best previously available tracers for that source.

  13. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    Energy Technology Data Exchange (ETDEWEB)

    Mike Bockelie; Dave Swensen; Martin Denison; Adel Sarofim; Connie Senior

    2004-12-22

    , immersive environment. The Virtual Engineering Framework (VEF), in effect a prototype framework, was developed through close collaboration with NETL supported research teams from Iowa State University Virtual Reality Applications Center (ISU-VRAC) and Carnegie Mellon University (CMU). The VEF is open source, compatible across systems ranging from inexpensive desktop PCs to large-scale, immersive facilities and provides support for heterogeneous distributed computing of plant simulations. The ability to compute plant economics through an interface that coupled the CMU IECM tool to the VEF was demonstrated, and the ability to couple the VEF to Aspen Plus, a commercial flowsheet modeling tool, was demonstrated. Models were interfaced to the framework using VES-Open. Tests were performed for interfacing CAPE-Open-compliant models to the framework. Where available, the developed models and plant simulations have been benchmarked against data from the open literature. The VEF has been installed at NETL. The VEF provides simulation capabilities not available in commercial simulation tools. It provides DOE engineers, scientists, and decision makers with a flexible and extensible simulation system that can be used to reduce the time, technical risk, and cost to develop the next generation of advanced, coal-fired power systems that will have low emissions and high efficiency. Furthermore, the VEF provides a common simulation system that NETL can use to help manage Advanced Power Systems Research projects, including both combustion- and gasification-based technologies.

  14. Realistic molecular model of kerogen's nanostructure.

    Science.gov (United States)

    Bousige, Colin; Ghimbeu, Camélia Matei; Vix-Guterl, Cathie; Pomerantz, Andrew E; Suleimenova, Assiya; Vaughan, Gavin; Garbarino, Gaston; Feygenson, Mikhail; Wildgruber, Christoph; Ulm, Franz-Josef; Pellenq, Roland J-M; Coasne, Benoit

    2016-05-01

    Despite kerogen's importance as the organic backbone for hydrocarbon production from source rocks such as gas shale, the interplay between kerogen's chemistry, morphology and mechanics remains unexplored. As the environmental impact of shale gas rises, identifying functional relations between its geochemical, transport, elastic and fracture properties from realistic molecular models of kerogens becomes all the more important. Here, by using a hybrid experimental-simulation method, we propose a panel of realistic molecular models of mature and immature kerogens that provide a detailed picture of kerogen's nanostructure without considering the presence of clays and other minerals in shales. We probe the models' strengths and limitations, and show that they predict essential features amenable to experimental validation, including pore distribution, vibrational density of states and stiffness. We also show that kerogen's maturation, which manifests itself as an increase in the sp(2)/sp(3) hybridization ratio, entails a crossover from plastic-to-brittle rupture mechanisms.

  15. Supercontinuum light sources for food analysis

    DEFF Research Database (Denmark)

    Møller, Uffe Visbech; Petersen, Christian Rosenberg; Kubat, Irnis

    2014-01-01

    . One track of Light & Food will target the mid-infrared spectral region. To date, the limitations of mid-infraredlight sources, such as thermal emitters, low-power laser diodes, quantum cascade lasers and synchrotron radiation, have precluded mid-IR applications where the spatial coherence, broad...... bandwidth,high brightness and portability of a supercontinuum laser are all required. DTU Fotonik has now demonstrated the first optical fiber based broadband supercontinuum light souce, which covers 1.4-13.3μm and thereby most of the molecular fingerprint region....

  16. Bringing high-performance computing to the biologist's workbench: approaches, applications, and challenges

    International Nuclear Information System (INIS)

    Oehmen, C S; Cannon, W R

    2008-01-01

    Data-intensive and high-performance computing are poised to significantly impact the future of biological research which is increasingly driven by the prevalence of high-throughput experimental methodologies for genome sequencing, transcriptomics, proteomics, and other areas. Large centers such as NIH's National Center for Biotechnology Information, The Institute for Genomic Research, and the DOE's Joint Genome Institute) have made extensive use of multiprocessor architectures to deal with some of the challenges of processing, storing and curating exponentially growing genomic and proteomic datasets, thus enabling users to rapidly access a growing public data source, as well as use analysis tools transparently on high-performance computing resources. Applying this computational power to single-investigator analysis, however, often relies on users to provide their own computational resources, forcing them to endure the learning curve of porting, building, and running software on multiprocessor architectures. Solving the next generation of large-scale biology challenges using multiprocessor machines-from small clusters to emerging petascale machines-can most practically be realized if this learning curve can be minimized through a combination of workflow management, data management and resource allocation as well as intuitive interfaces and compatibility with existing common data formats

  17. Investigating the Fundamentals of Molecular Depth Profiling Using Strong-field Photoionization of Sputtered Neutrals

    Science.gov (United States)

    Willingham, D.; Brenes, D. A.; Winograd, N.; Wucher, A.

    2010-01-01

    Molecular depth profiles of model organic thin films were performed using a 40 keV C60+ cluster ion source in concert with TOF-SIMS. Strong-field photoionization of intact neutral molecules sputtered by 40 keV C60+ primary ions was used to analyze changes in the chemical environment of the guanine thin films as a function of ion fluence. Direct comparison of the secondary ion and neutral components of the molecular depth profiles yields valuable information about chemical damage accumulation as well as changes in the molecular ionization probability. An analytical protocol based on the erosion dynamics model is developed and evaluated using guanine and trehalose molecular secondary ion signals with and without comparable laser photoionization data. PMID:26269660

  18. IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface.

    Science.gov (United States)

    Sun, Yin Xue; Huang, Yan Xin; Li, Feng Li; Wang, Hong Yan; Fan, Cong; Bao, Yong Li; Sun, Lu Guo; Ma, Zhi Qiang; Kong, Jun; Li, Yu Xin

    2012-01-05

    The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

  19. Radiation degradation of molasses pigment. 2. Molecular weight fraction

    International Nuclear Information System (INIS)

    Sawai, Teruko; Sekiguchi, Masayuki; Tanabe, Hiroko

    1996-01-01

    Water demand in Tokyo has increased rapidly. Because of the scarcity of water sources within the city, Tokyo is dependent on water from other prefectures. Recycling of municipal effluent is an effective means of coping with water shortage in Tokyo. We have studied the radiation treatment of waste water for recycling. The degradation of molasses pigments in waste water from yeast factory by radiation was investigated. The dialyzed molasses pigments and non-dialyzed samples in waste waters were compared in chromaticity, UV absorption, color different and COD. The dialysis and fractionation by permeable membrane were carried out with Seamless Cellulose tubing (Union Carbide Corporation) and spectra/Por membrane (Spectrum Medical Industries INC.) The TOC values decreased and the dark brown color faded with increasing dose. The high molecular weight components of molasses pigment were degraded to lower molecular weight substances and decomposed to carbon dioxide. The relationships between the value of chromaticity/TOC and molecular weight of molasses pigments were obtained by radiation. (author)

  20. An open source digital servo for atomic, molecular, and optical physics experiments

    Energy Technology Data Exchange (ETDEWEB)

    Leibrandt, D. R., E-mail: david.leibrandt@nist.gov; Heidecker, J. [National Institute of Standards and Technology, Boulder, Colorado 80305 (United States)

    2015-12-15

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of {sup 27}Al{sup +} in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

  1. An open source digital servo for atomic, molecular, and optical physics experiments

    International Nuclear Information System (INIS)

    Leibrandt, D. R.; Heidecker, J.

    2015-01-01

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27 Al + in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser

  2. An open source digital servo for atomic, molecular, and optical physics experiments

    Science.gov (United States)

    Leibrandt, D. R.; Heidecker, J.

    2015-12-01

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27Al+ in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

  3. Molecular oncology focus - Is carcinogenesis a 'mitochondriopathy'?

    Directory of Open Access Journals (Sweden)

    Ścińska Anna

    2010-04-01

    Full Text Available Abstract Mitochondria are sub-cellular organelles that produce adenosine triphosphate (ATP through oxidative phosphorylation (OXPHOS. As suggested over 70 years ago by Otto Warburg and recently confirmed with molecular techniques, alterations in respiratory activity and in mitochondrial DNA (mtDNA appear to be common features of malignant cells. Somatic mtDNA mutations have been reported in many types of cancer cells, and some reports document the prevalence of inherited mitochondrial DNA polymorphisms in cancer patients. Nevertheless, a careful reanalysis of methodological criteria and methodology applied in those reports has shown that numerous papers can't be used as relevant sources of data for systematic review, meta-analysis, or finally for establishment of clinically applicable markers. In this review technical and conceptual errors commonly occurring in the literature are summarized. In the first place we discuss, why many of the published papers cannot be used as a valid and clinically useful sources of evidence in the biomedical and healthcare contexts. The reasons for introduction of noise in data and in consequence - bias for the interpretation of the role of mitochondrial DNA in the complex process of tumorigenesis are listed. In the second part of the text practical aspects of mtDNA research and requirements necessary to fulfill in order to use mtDNA analysis in clinics are shown. Stringent methodological criteria of a case-controlled experiment in molecular medicine are indicated. In the third part we suggest, what lessons can be learned for the future and propose guidelines for mtDNA analysis in oncology. Finally we conclude that, although several conceptual and methodological difficulties hinder the research on mitochondrial patho-physiology in cancer cells, this area of molecular medicine should be considered of high importance for future clinical practice.

  4. New trends in atomic and molecular physics. Advanced technological applications

    International Nuclear Information System (INIS)

    Mohan, Man

    2013-01-01

    Represents an up-to-date scientific status report on new trends in atomic and molecular physics. Multi-disciplinary approach. Also of interest to researchers in astrophysics and fusion plasma physics. Contains material important for nano- and laser technology. The field of Atomic and Molecular Physics (AMP) has reached significant advances in high-precision experimental measurement techniques. The area covers a wide spectrum ranging from conventional to new emerging multi-disciplinary areas like physics of highly charged ions (HCI), molecular physics, optical science, ultrafast laser technology etc. This book includes the important topics of atomic structure, physics of atomic collision, photoexcitation, photoionization processes, Laser cooling and trapping, Bose Einstein condensation and advanced technology applications of AMP in the fields of astronomy, astrophysics, fusion, biology and nanotechnology. This book is useful for researchers, professors, graduate, post graduate and PhD students dealing with atomic and molecular physics. The book has a wide scope with applications in neighbouring fields like plasma physics, astrophysics, cold collisions, nanotechnology and future fusion energy sources like ITER (international Thermonuclear Experimental Reactor) Tokomak plasma machine which need accurate AMP data.

  5. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Farmer, B.J.

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  6. Bibliography of atomic and molecular processes. Volume 1, 1978-1981

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Farmer, B.J. (comps.)

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  7. Ochratoxin A: General Overview and Actual Molecular Status

    International Nuclear Information System (INIS)

    El Khoury, A.; Atoui, A.

    2010-01-01

    Ochratoxin A (OTA) is a mycotoxin produced by several species of Aspergillus and Penicillium fungi that structurally consists of a para-chlorophenolic group containing a dihydroisocoumarin moiety that is amide-linked to L-phenylalanine. OTA is detected worldwide in various food and feed sources. Studies show that this molecule can have several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic. A role in the etiology of Balkan endemic nephropathy and its association to urinary tract tumors has been also proved. In this review, we will explore the general aspect of OTA: physico-chemical properties, toxicological profile, OTA producing fungi, contaminated food, regulation, legislation and analytical methods. Due to lack of sufficient information related to the molecular background, this paper will discuss in detail the recent advances in molecular biology of OTA biosynthesis, based on information and on new data about identification and characterization of ochratoxin biosynthetic genes in both Penicillium and Aspergillus species. This review will also cover the development of the molecular methods for the detection and quantification of OTA producing fungi in various foodstuffs. (author)

  8. Infrared studies of the S235 molecular cloud

    International Nuclear Information System (INIS)

    Evans, N.J. II; Beichman, C.; Gatley, I.; Harvey, P.; Nadeau, D.; Sellgren, K.

    1981-01-01

    Infrared observations from 7.8 to 200 μm have been obtained for the S235 molecular cloud. Far-infrared maps were obtained for a region of active star formation, as marked by the presence of compact H II regions, water masers, and compact near-infrared sources. The primary heating source for the far-infrared emission appears to be the compact H II region, S235A. Detailed examination of the gas energetics in the region supports the plausibility of the picture in which the gas is heated by collisions with warm dust grains. The ratio of far-infrared optical depth to 13 CO column density is somewhat lower in this source than is commonly found. This effect may be caused by the presence of substantial 13 CO in regions where the dust is not warm enough to emit substantial 50--100 μm radiation

  9. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  10. MILKY WAY STAR-FORMING COMPLEXES AND THE TURBULENT MOTION OF THE GALAXY'S MOLECULAR GAS

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eve J.; Rahman, Mubdi [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON, M5S 3H4 (Canada); Murray, Norman, E-mail: elee@astro.utoronto.ca, E-mail: rahman@astro.utoronto.ca, E-mail: elee@cita.utoronto.ca, E-mail: murray@cita.utoronto.ca [Canadian Institute for Theoretical Astrophysics, 60 St. George Street, University of Toronto, Toronto, ON, M5S 3H8 (Canada)

    2012-06-20

    We analyze Spitzer GLIMPSE, Midcourse Space Experiment (MSX), and Wilkinson Microwave Anisotropy Probe (WMAP) images of the Milky Way to identify 8 {mu}m and free-free sources in the Galaxy. Seventy-two of the 88 WMAP sources have coverage in the GLIMPSE and MSX surveys suitable for identifying massive star-forming complexes (SFCs). We measure the ionizing luminosity functions of the SFCs and study their role in the turbulent motion of the Galaxy's molecular gas. We find a total Galactic free-free flux f{sub {nu}} = 46,177.6 Jy; the 72 WMAP sources with full 8 {mu}m coverage account for 34,263.5 Jy ({approx}75%), with both measurements made at {nu} = 94 GHz (W band). We find a total of 280 SFCs, of which 168 have unique kinematic distances and free-free luminosities. We use a simple model for the radial distribution of star formation to estimate the free-free and ionizing luminosity for the sources lacking distance determinations. The total dust-corrected ionizing luminosity is Q = (2.9 {+-} 0.5) Multiplication-Sign 10{sup 53} photons s{sup -1}, which implies a Galactic star formation rate of M-dot{sub *}= 1.2{+-}0.2 M{sub Sun} yr{sup -1}. We present the (ionizing) luminosity function of the SFCs and show that 24 sources emit half the ionizing luminosity of the Galaxy. The SFCs appear as bubbles in GLIMPSE or MSX images; the radial velocities associated with the bubble walls allow us to infer the expansion velocity of the bubbles. We calculate the kinetic luminosity of the bubble expansion and compare it to the turbulent luminosity of the inner molecular disk. SFCs emitting 80% of the total Galactic free-free luminosity produce a kinetic luminosity equal to 65% of the turbulent luminosity in the inner molecular disk. This suggests that the expansion of the bubbles is a major driver of the turbulent motion of the inner Milky Way molecular gas.

  11. Dietary carbohydrate source influences molecular fingerprints of the rat faecal microbiota

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Hansen, Max; Poulsen, Morten

    2006-01-01

    Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan) or olig......Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan...... of coliform bacteria in faeces. In the inulin and oligofructose groups, higher levels of butyrate and propionate, respectively, were measured. Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR amplified bacterial 16S rRNA genes...... and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though...

  12. Herbig-haro objects and mid-infrared outflows in the VELA C molecular cloud

    International Nuclear Information System (INIS)

    Zhang, Miaomiao; Wang, Hongchi; Henning, Thomas

    2014-01-01

    We have performed a deep [S II] λλ6717/6731 wide field Herbig-Haro (HH) object survey toward the Vela C molecular cloud with a sky coverage of about 2 deg 2 . In total, 18 new HH objects, HH 1090-1107, are discovered and the two previously known HH objects, HH 73-74, are also detected in our [S II] images. We also present an investigation of mid-infrared outflows in the Vela C molecular cloud using the Wide-field Infrared Survey Explorer images taken from AllWISE data release. Using the method suggested by Zhang and Wang, 11 extended green objects (EGOs) are identified to be the mid-infrared outflows, including 6 new mid-infrared outflows that have not been detected previously at other wavelengths and 5 mid-infrared counterparts of the HH objects detected in this work. Using the AllWISE Source Catalog and the source classification scheme suggested by Koenig et al., we have identified 56 young stellar object (YSO) candidates in the Vela C molecular cloud. The possible driving sources of the HH objects and EGOs are discussed based on the morphology of HH objects and EGOs and the locations of HH objects, EGOs and YSO candidates. Finally we associate 12 HH objects and 5 EGOs with 10 YSOs and YSO candidates. The median length of the outflows in Vela C is 0.35 pc and the outflows seem to be oriented randomly.

  13. Small Galactic H II regions. II. The molecular clouds and star formation

    International Nuclear Information System (INIS)

    Hunter, D.A.; Thronson, H.A. Jr.; Wilton, C.

    1990-01-01

    CO maps of molecular clouds associated with 11 small Galactic H II regions are presented and compared with IR images obtained by IRAS. The molecular masses of the clouds are computed and compared with the masses of the stellar content. The mapped clouds have masses of 1000-60,000 solar and are typical of the more numerous, smaller Galactic molecular clouds. All of the clouds have recently made massive OB stars, and many have complex spatial and kinematic structures. The coincidence of IRAS sources and CO peaks suggests that many of the clouds have sites of star formation other than the optically visible H II region. Star-formation efficiencies are uncertain, with values for the clouds ranging from 0.02 to 0.6 with an average value of 0.2. There is no trend of the upper stellar mass limit with Galactic radius and with molecular cloud mass. 53 refs

  14. Quantitative study of luminescence optical tomography. Application to sources localisation in molecular imaging

    International Nuclear Information System (INIS)

    Boffety, Matthieu

    2010-01-01

    Molecular imaging is a major modality in the field of preclinical research. Among the existing methods, techniques based on optical detection of visible or near infrared radiation are the most recent and are mainly represented by luminescence optical tomography techniques. These methods allow for 3D characterization of a biological medium by reconstructing maps of concentration or localisation of luminescent beacons sensitive to biological and chemical processes at the molecular or cellular scale. Luminescence optical tomography is based on a model of light propagation in tissues, a protocol for acquiring surface signal and a numerical inversion procedure used to reconstruct the parameters of interest. This thesis is structured around these three axes and provides an answer to each problem. The main objective of this study is to introduce and present the tools to evaluate the theoretical performances of optical tomography methods. One of its major outcomes is the realisation of experimental tomographic reconstructions from images acquired by an optical imager designed for 2D planar imaging and developed by the company Quidd. In a first step we develop the theory of transport in scattering medium to establish the concept on which our work will rely. We present two different propagation models as well as resolution methods and theoretical difficulties associated with them. In a second part we introduce the statistical tools used to characterise tomographic systems. We define and apply a procedure to simple situations in luminescence optical tomography. The last part of this work presents the development of an inversion procedure. After introducing the theoretical framework we validate the procedure from numerical data before successfully applying it to experimental measurements. (author) [fr

  15. Source investigation of two outbreaks of skin and soft tissue infection by Mycobacterium abscessus subsp. abscessus in Venezuela.

    Science.gov (United States)

    Torres-Coy, J A; Rodríguez-Castillo, B A; Pérez-Alfonzo, R; DE Waard, J H

    2016-04-01

    Outbreaks of soft tissue or skin infection due to non-tuberculous mycobacteria are reported frequently in scientific journals but in general the infection source in these outbreaks remains unknown. In Venezuela, in two distinct outbreaks, one after breast augmentation surgery and another after hydrolipoclasy therapy, 16 patients contracted a soft tissue infection due to Mycobacterium abscessus subsp. abscessus. Searching for the possible environmental infection sources in these outbreaks, initially the tap water (in the hydrolipoclasy therapy outbreak) and a surgical skin marker (in the breast implant surgery outbreak), were identified as the infection sources. Molecular typing of the strains with a variable number tandem repeat typing assay confirmed the tap water as the infection source but the molecular typing technique excluded the skin marker. We discuss the results and make a call for the implementation of stringent hygiene and disinfection guidelines for cosmetic procedures in Venezuela.

  16. Dynamics of infrared multiphonon dissociation of SF6 by molecular beam method

    International Nuclear Information System (INIS)

    Grant, E.R.; Coggiola, M.J.; Lee, Y.T.; Schulz, P.A.; Shen, Y.R.

    1977-01-01

    A crossed molecular beam apparatus has been adapted to study the dynamics of excitation and dissociation of polyatomic molecules in intense IR laser fields. Initial experiments have involved the study of the dissociation of SF 6 by CO 2 laser radiation at 10.6 μm. A molecular beam of SF 6 was formed by supersonic expansion using three stages of differential pumping. A grating tuned pulsed CO 2 TEA laser was used as the excitation source. The laser beam was focused by a 25 cm focal length ZnSe lens, and crossed the molecular beam near its focal point. The fragments produced by multiphonon dissociation of SF 6 within the small interaction region were detected as a function of recoil angle and velocity. (Auth.)

  17. An Assessment of Air As a Source of DNA Contamination Encountered When Performing PCR

    OpenAIRE

    Witt, Nina; Rodger, Gillian; Vandesompele, Jo; Benes, Vladimir; Zumla, Alimuddin; Rook, Graham A.; Huggett, Jim F.

    2009-01-01

    Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as...

  18. Organic composition and source apportionment of fine aerosol at Monterrey, Mexico, based on organic markers

    Directory of Open Access Journals (Sweden)

    Y. Mancilla

    2016-01-01

    Full Text Available Primary emissions from anthropogenic and biogenic sources as well as secondary formation are responsible for the pollution levels of ambient air in major urban areas. These sources release fine particles into the air that negatively impact human health and the environment. Organic molecular markers, which are compounds that are unique to specific PM2.5 sources, can be utilized to identify the major emission sources in urban areas. In this study, 43 representative PM2.5 samples, for both daytime and nighttime periods, were built from individual samples collected in an urban site of the Monterrey metropolitan area (MMA during the spring and fall of 2011 and 2012. The samples were analyzed for organic carbon, elemental carbon, and organic molecular markers. Several diagnostic tools were employed for the preliminary identification of emission sources. Organic compounds for eight compound classes were quantified. The n-alkanoic acids were the most abundant, followed by n-alkanes, wood smoke markers, and levoglucosan/alkenoic acids. Polycyclic aromatic hydrocarbons (PAHs and hopanes were less abundant. The carbon preference index (0.7–2.6 for n-alkanes indicates a major contribution of anthropogenic and mixed sources during the fall and the spring, respectively. Hopanes levels confirmed the contribution from gasoline and diesel engines. In addition, the contribution of gasoline and diesel vehicle exhaust was confirmed and identified by the PAH concentrations in PM2.5. Diagnostic ratios of PAHs showed emissions from burning coal, wood, biomass, and other fossil fuels. The total PAHs and elemental carbon were correlated (r2 =  0.39–0.70 across the monitoring periods, reinforcing that motor vehicles are the major contributors of PAHs. Cholesterol levels remained constant during the spring and fall, showing evidence of the contribution of meat-cooking operations, while the isolated concentrations of levoglucosan suggested occasional biomass

  19. High resolution far-infrared survey of A section of the galactic plane. I. The nature of the sources

    International Nuclear Information System (INIS)

    Jaffe, D.T.; Stier, M.T.; Fazio, G.G.

    1982-01-01

    We have surveyed a 7.5 deg 2 portion of the galactic plane between l/sup II/ = 10 0 and l/sup II/ = 16 0 at 70 μm with a 1' beam. We present far-infrared, radio continuum, and 12 CO and 13 CO line observations of the 42 far-infrared sources in the survey region. The sources range in luminosity from 4 x 10 3 to 3 x 10 6 L/sub sun/. Most are associated with 12 CO peaks. More than half of the sources have associated H 2 O maser emission. Half have associated radio continuum emission at a limit of 100 mJy. Eight sources have radio emission at weaker levels. In a number of cases, the far-infrared source is smaller than its associated radio source. This difference can be explained in the context of the ''blister'' picture of H II regions. One group of sources emits many fewer Lyman continuum photons than expected, given the far-infrared luminosities. We examine a number of possible reasons for this and conclude that the most reasonable explanation is that clusters of early type stars rather than single stars excite the far-infrared sources. We examine the energetics in the molecular clouds surrounding the infrared sources and conclude that the sources could supply the energy to explain the observed temperature structure and velocity field in the molecular gas

  20. Optical Imaging of Ionizing Radiation from Clinical Sources.

    Science.gov (United States)

    Shaffer, Travis M; Drain, Charles Michael; Grimm, Jan

    2016-11-01

    Nuclear medicine uses ionizing radiation for both in vivo diagnosis and therapy. Ionizing radiation comes from a variety of sources, including x-rays, beam therapy, brachytherapy, and various injected radionuclides. Although PET and SPECT remain clinical mainstays, optical readouts of ionizing radiation offer numerous benefits and complement these standard techniques. Furthermore, for ionizing radiation sources that cannot be imaged using these standard techniques, optical imaging offers a unique imaging alternative. This article reviews optical imaging of both radionuclide- and beam-based ionizing radiation from high-energy photons and charged particles through mechanisms including radioluminescence, Cerenkov luminescence, and scintillation. Therapeutically, these visible photons have been combined with photodynamic therapeutic agents preclinically for increasing therapeutic response at depths difficult to reach with external light sources. Last, new microscopy methods that allow single-cell optical imaging of radionuclides are reviewed. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  1. NATO Advanced Study Institute on Molecular Physics and Hypersonic Flows

    CERN Document Server

    1996-01-01

    Molecular Physics and Hypersonic Flows bridges the gap between the fluid dynamics and molecular physics communities, emphasizing the role played by elementary processes in hypersonic flows. In particular, the work is primarily dedicated to filling the gap between microscopic and macroscopic treatments of the source terms to be inserted in the fluid dynamics codes. The first part of the book describes the molecular dynamics of elementary processes both in the gas phase and in the interaction with surfaces by using quantum mechanical and phenomenological approaches. A second group of contributions describes thermodynamics and transport properties of air components, with special attention to the transport of internal energy. A series of papers is devoted to the experimental and theoretical study of the flow of partially ionized gases. Subsequent contributions treat modern computational techniques for 3-D hypersonic flow. Non-equilibrium vibrational kinetics are then described, together with the coupling of vibra...

  2. Ultrafast studies of dynamic & complex systems: Understanding molecular and ionization dynamics

    OpenAIRE

    Hockett, Paul

    2016-01-01

    Presentation given at the ITAMP workshop "Ultrafast atomic and molecular physics with cutting-edge light sources: New opportunities and challenges", held at Kansas State University, Nov. 2013.  A video of the presentation can be found on the ITAMP Youtube channel, https://www.youtube.com/watch?v=x8RWWDWZJpk

  3. H2O sources in regions of star formation

    International Nuclear Information System (INIS)

    Lo, K.Y.; Burke, B.F.; Haschick, A.D.

    1975-01-01

    Regions and objects believed to be in early stages of stellar formation have been searched for H 2 O 22-GHz line emission with the Haystack 120-foot (37 m) telescope. The objects include radio condensations, infrared objects in H ii regions, and Herbig-Haro objects. Nine new H 2 O sources were detected in the vicinity of such objects, including the Sharpless H ii regions S152, S235, S255, S269, G45.1+0.1, G45.5+0.1, AFCRL infrared object No. 809--2992, and Herbig-Haro objects 1 and 9. The new H 2 O sources detected in H ii regions are associated, but not coincident, with the the radio condensations. Water vapor line emission was detected in approx.25 percent of the regions searched. The association of H 2 O sources with regions of star formation is taken to be real. The spatial relationship of H 2 O sources to infrared objects, radio condensations, class I OH sources, and molecular clouds are discussed. The suggestion is made that an H 2 O source may be excited by a highly obscured star of extreme youth

  4. H- Ion Sources For CERN’s Linac4

    CERN Document Server

    Lettry, J; Coutron, Y; Chaudeta, E; Dallocchio, A; Gil Flores, J; Hansen, J; Mahner, E; Mathot, S; Mattei, S; Midttun, O; Moyret, P; Nisbet, D; O’Neil, M; Paoluzzi, M; Pasquino, C; Pereira, H; Sanchez Arias, J; Schmitzer, C; Scrivens, R; Steyaert, D

    2013-01-01

    The specifications set to the Linac4 ion source are: H- ion pulses of 0.5 ms duration, 80 mA intensity and 45 keV energy within a normalized emittance of 0.25 mmmrad RMS at a repetition rate of 2 Hz. In 2010, during the commissioning of a prototype based on H- production from the plasma volume, it was observed that the powerful co-extracted electron beam inherent to this type of ion source could destroy its electron beam dump well before reaching nominal parameters. However, the same source was able to provide 80 mA of protons mixed with a small fraction of H2+ and H3+ molecular ions. The commissioning of the radio frequency quadrupole accelerator (RFQ), beam chopper and H- beam diagnostics of the Linac4 are scheduled for 2012 and its final installation in the underground building is to start in 2013. Therefore, a crash program was launched in 2010 and reviewed in 2011 aiming at keeping the original Linac4 schedule with the following deliverables: Design and production of a volume ion source prototype suitabl...

  5. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking.

    Science.gov (United States)

    Ferrari, Rafaela G; Panzenhagen, Pedro H N; Conte-Junior, Carlos A

    2017-01-01

    Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

  6. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

    Directory of Open Access Journals (Sweden)

    Rafaela G. Ferrari

    2017-12-01

    Full Text Available Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models. Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

  7. EAACI Molecular Allergology User's Guide.

    Science.gov (United States)

    Matricardi, P M; Kleine-Tebbe, J; Hoffmann, H J; Valenta, R; Hilger, C; Hofmaier, S; Aalberse, R C; Agache, I; Asero, R; Ballmer-Weber, B; Barber, D; Beyer, K; Biedermann, T; Bilò, M B; Blank, S; Bohle, B; Bosshard, P P; Breiteneder, H; Brough, H A; Caraballo, L; Caubet, J C; Crameri, R; Davies, J M; Douladiris, N; Ebisawa, M; EIgenmann, P A; Fernandez-Rivas, M; Ferreira, F; Gadermaier, G; Glatz, M; Hamilton, R G; Hawranek, T; Hellings, P; Hoffmann-Sommergruber, K; Jakob, T; Jappe, U; Jutel, M; Kamath, S D; Knol, E F; Korosec, P; Kuehn, A; Lack, G; Lopata, A L; Mäkelä, M; Morisset, M; Niederberger, V; Nowak-Węgrzyn, A H; Papadopoulos, N G; Pastorello, E A; Pauli, G; Platts-Mills, T; Posa, D; Poulsen, L K; Raulf, M; Sastre, J; Scala, E; Schmid, J M; Schmid-Grendelmeier, P; van Hage, M; van Ree, R; Vieths, S; Weber, R; Wickman, M; Muraro, A; Ollert, M

    2016-05-01

    The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology User's Guide (MAUG) provides comprehensive information on important allergens and describes the diagnostic options using CRD. Part A of the EAACI MAUG introduces allergen molecules, families, composition of extracts, databases, and diagnostic IgE, skin, and basophil tests. Singleplex and multiplex IgE assays with components improve both sensitivity for low-abundance allergens and analytical specificity; IgE to individual allergens can yield information on clinical risks and distinguish cross-reactivity from true primary sensitization. Part B discusses the clinical and molecular aspects of IgE-mediated allergies to foods (including nuts, seeds, legumes, fruits, vegetables, cereal grains, milk, egg, meat, fish, and shellfish), inhalants (pollen, mold spores, mites, and animal dander), and Hymenoptera venom. Diagnostic algorithms and short case histories provide useful information for the clinical workup of allergic individuals targeted for CRD. Part C covers protein families containing ubiquitous, highly cross-reactive panallergens from plant (lipid transfer proteins, polcalcins, PR-10, profilins) and animal sources (lipocalins, parvalbumins, serum albumins, tropomyosins) and explains their diagnostic and clinical utility. Part D lists 100 important allergen molecules. In conclusion, IgE-mediated reactions and allergic diseases, including allergic rhinoconjunctivitis, asthma, food reactions, and insect sting reactions, are discussed from a novel molecular perspective. The EAACI MAUG documents the rapid progression of molecular allergology from basic research to its integration into clinical practice, a quantum leap in the management of allergic patients. © 2016 John Wiley

  8. Molecular Mechanism and Genetic Determinants of Buprofezin Degradation

    OpenAIRE

    Chen, Xueting; Ji, Junbin; Zhao, Leizhen; Qiu, Jiguo; Dai, Chen; Wang, Weiwu; He, Jian; Jiang, Jiandong; Hong, Qing; Yan, Xin

    2017-01-01

    Buprofezin is a widely used insect growth regulator whose residue has been frequently detected in the environment, posing a threat to aquatic organisms and nontarget insects. Microorganisms play an important role in the degradation of buprofezin in the natural environment. However, the relevant catabolic pathway has not been fully characterized, and the molecular mechanism of catabolism is still completely unknown. Rhodococcus qingshengii YL-1 can utilize buprofezin as a sole source of carbon...

  9. A New Molecular Surveillance System for Leishmaniasis

    Science.gov (United States)

    Pandey, Kishor; Pandey, Basu Dev; Mallik, Arun Kumar; Acharya, Jyoti; Kato, Kentaro; Kaneko, Osamu; Ferreira, Pedro Eduardo

    2014-01-01

    Abstract. Presently, global efforts are being made to control and eradicate the deadliest tropical diseases through the improvement of adequate interventions. A critical point for programs to succeed is the prompt and accurate diagnosis in endemic regions. Rapid diagnostic tests (RDTs) are being massively deployed and used to improve diagnosis in tropical countries. In the present report, we evaluated the hypothesis of, after use for diagnosis, the reuse of the Leishmania RDT kit as a DNA source, which can be used downstream as a molecular surveillance and/or quality control tool. As a proof of principle, a polymerase chain reaction-based method was used to detect Leishmania spp. minicircle kinetoplast DNA from leishmaniasis RDT kits. Our results show that Leishmania spp. DNA can be extracted from used RDTs and may constitute an important, reliable, and affordable tool to assist in future leishmaniasis molecular surveillance methods. PMID:24752687

  10. SEASONAL ABUNDANCE OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    Science.gov (United States)

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...

  11. Ten years of surveillance of the Yulong plague focus in China and the molecular typing and source tracing of the isolates.

    Science.gov (United States)

    Wang, Peng; Shi, Liyuan; Zhang, Fuxin; Guo, Ying; Zhang, Zhikai; Tan, Hongli; Cui, Zhigang; Ding, Yibo; Liang, Ying; Liang, Yun; Yu, Dongzheng; Xu, Jianguo; Li, Wei; Song, Zhizhong

    2018-03-01

    Plague, caused by Yersinia pestis, was classified as a reemerging infectious disease by the World Health Organization. The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province, China. Thereafter, continuous wild rodent plague (sylvatic plague) was identified as the main plague reservoir of this focus. In this study, the epizootics in Yulong focus were described, and three molecular typing methods, including the different region (DFR) analysis, clustered regularly interspaced short palindromic repeats (CRISPRs), and the multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) (14+12), were used for the molecular typing and source tracing of Y. pestis isolates in the Yulong plague focus. Simultaneously, several isolates from the vicinity of Yunnan were used as controls. The results showed that during the 10-year period from 2006 to 2016, an animal plague epidemic occurred in 6 of those years, and 5 villages underwent an animal plague epidemic within a 30-km2 area of the Yulong plague focus. Searching for dead mice was the most effective monitoring method in this plague focus. No positive sample has been found in 6937 captured live rodents thus far, suggesting that the virulence of strains in the Yulong plague focus is stronger and the survival time of mice is shorter after infection. Strains from Lijiang, Sichuan and Tibet were of the same complex based on a typing analysis of DFR and CRISPR. The genetic relationship of Y. pestis illustrated by MLVA "14+12" demonstrates that Tibet and Sichuan strains evolved from the strains 1.IN2 (Qinghai, 1970 and Tibet, 1976), and Lijiang strains are closer to Batang strains (Batang County in Sichuan province, 2011, Himalaya marmot plague foci) in terms of genetic or phylogenic relationships. In conclusion, we have a deeper understanding of this new plague focus throughout this study, which provides a basis for effective prevention and

  12. Investigation and Applications of In-Source Oxidation in Liquid Sampling-Atmospheric Pressure Afterglow Microplasma Ionization (LS-APAG) Source.

    Science.gov (United States)

    Xie, Xiaobo; Wang, Zhenpeng; Li, Yafeng; Zhan, Lingpeng; Nie, Zongxiu

    2017-06-01

    A liquid sampling-atmospheric pressure afterglow microplasma ionization (LS-APAG) source is presented for the first time, which is embedded with both electrospray ionization (ESI) and atmospheric pressure afterglow microplasma ionization (APAG) techniques. This ion source is capable of analyzing compounds with diverse molecule weights and polarities. An unseparated mixture sample was detected as a proof-of-concept, giving complementary information (both polarities and non-polarities) with the two ionization modes. It should also be noted that molecular mass can be quickly identified by ESI with clean and simple spectra, while the structure can be directly studied using APAG with in-source oxidation. The ionization/oxidation mechanism and applications of the LS-APAG source have been further explored in the analysis of nonpolar alkanes and unsaturated fatty acids/esters. A unique [M + O - 3H] + was observed in the case of individual alkanes (C 5 -C 19 ) and complex hydrocarbons mixture under optimized conditions. Moreover, branched alkanes generated significant in-source fragments, which could be further applied to the discrimination of isomeric alkanes. The technique also facilitates facile determination of double bond positions in unsaturated fatty acids/esters due to diagnostic fragments (the acid/ester-containing aldehyde and acid oxidation products) generated by on-line ozonolysis in APAG mode. Finally, some examples of in situ APAG analysis by gas sampling and surface sampling were given as well. Graphical Abstract ᅟ.

  13. Investigation of fingerprints for small polar molecules by using a tunable monochromatic THz source

    Science.gov (United States)

    Sun, Hongqian

    Over the past 20 years, considerable efforts have been dedicated to the generation and the application of electromagnetic waves in the Terahertz (THz) regime. Among all of the proposed applications, the THz spectroscopy is probably the most mature and promising one. According to the previous reports, the THz spectroscopy has been extensively applied into many analysis fields, including the investigation of vibrational modes for the crystalline solids, the characterization of electron transport in the condense matters and the identification of explosive materials at a standoff distance. More interestingly, since most gas phase chemicals exhibit unique transition peaks in the THz spectra, one could in principle achieve highly accurate molecular fingerprinting and chemical sensing as well. However, all of the practical THz spectroscopy applications were still greatly hampered by the lack of suitable sources and detectors. In this thesis, a unique approach to measure the THz spectrum is developed based on a novel tunable narrowband source. Unlike the previous THz systems, high power THz pulses were generated by the difference frequency generation processes between two collinearly propagated near infrared laser beams. To tune the output THz signal frequency, one can simply adjust one of the incident beam frequencies. Therefore, based on a convenient wavelength tuning scheme, the transmission spectra can be measured for a series of polar gases with either similar or distinct molecular structures. According to the measured spectra, it is found that the obtained transition frequencies, absorption intensities and molecular constants are all in good agreement with the theoretical results tabulated in the molecular spectroscopic databases, such as the HITRAN database. By further analyzing the transition frequencies, it is also discovered that one can confidently identify each polar molecule and differentiate between various isotopic variants based on their characteristic

  14. Molecular Epidemiology of Plasmodium falciparum Malaria Outbreak, Tumbes, Peru, 2010–2012

    Science.gov (United States)

    Okoth, Sheila Akinyi; Arrospide, Nancy; Gonzalez, Rommell V.; Sánchez, Juan F.; Macedo, Silvia; Conde, Silvia; Tapia, L. Lorena; Salas, Carola; Gamboa, Dionicia; Herrera, Yeni; Edgel, Kimberly A.; Udhayakumar, Venkatachalam; Lescano, Andrés G.

    2015-01-01

    During 2010–2012, an outbreak of 210 cases of malaria occurred in Tumbes, in the northern coast of Peru, where no Plasmodium falciparum malaria case had been reported since 2006. To identify the source of the parasite causing this outbreak, we conducted a molecular epidemiology investigation. Microsatellite typing showed an identical genotype in all 54 available isolates. This genotype was also identical to that of parasites isolated in 2010 in the Loreto region of the Peruvian Amazon and closely related to clonet B, a parasite lineage previously reported in the Amazon during 1998–2000. These findings are consistent with travel history of index case-patients. DNA sequencing revealed mutations in the Pfdhfr, Pfdhps, Pfcrt, and Pfmdr1 loci, which are strongly associated with resistance to chloroquine and sulfadoxine/pyrimethamine, and deletion of the Pfhrp2 gene. These results highlight the need for timely molecular epidemiology investigations to trace the parasite source during malaria reintroduction events. PMID:25897626

  15. Combustion inputs into a terrestrial archive over 265 years as evidenced by BPCA molecular markers

    Science.gov (United States)

    Hanke, Ulrich M.; Eglinton, Timothy I.; Wiedemeier, Daniel B.; Schmidt, Michael W. I.

    2015-04-01

    Pyrogenic organic matter (PyOM) such as char and soot is produced during the incomplete combustion of biomass and fossil fuel. It is composed of condensed aromatic structures and can resist degradation processes, maybe over long periods of time. Land-use changes, industrial activity and its transport by wind and water affect the fluxes of PyOM from the source to its sedimentary archive. Investigating environmental PyOM with the molecular marker benzene polycarboxylic acid (BPCA) method provides various information about quantity, quality (BPCA distribution pattern) and about its isotopic composition (13C and 14C). Assessing PyOM quality can indicate whether it is mostly combustion condensate (soot) or combustion residue (charcoal) and potentially allow source apportionment. Our study area is the Pettaquamscutt River catchment area (35 km2), Rhode Island, U.S.A. It is located down-wind of industrial areas recording deposition of long-distance atmospheric transport as well as local catchment inputs, both from natural and anthropogenic sources. We investigated 50 samples of a sediment record over a time span of 265 years (1733-1998 AD). Previous investigations provided information on the age of deposition, the content of polycyclic aromatic hydrocarbons (PAH) as well as of the radiocarbon contents of total organic carbon (TOC) and PAH (Lima, 2004). We used the BPCA molecular marker method to quantify and characterize PyOM in the same record. First results show that quantity and quality of PyOM change over 265 years. Our investigation aims at understanding how different sources of PyOM are reflected in terrestrial archives by comparing the results of BPCA with radiocarbon-dated TOC and PAH records. Among other aspects, the PAH record reflects the Great Depression and the 1970s oil embargo in North America. We interpret the BPCA distribution patterns regarding the simultaneous shift of dominant fuels including wood, coal, petroleum and gas. Future work will include

  16. Where is OH and Does It Trace the Dark Molecular Gas (DMG)?

    Science.gov (United States)

    Li, Di; Tang, Ningyu; Nguyen, Hiep; Dawson, J. R.; Heiles, Carl; Xu, Duo; Pan, Zhichen; Goldsmith, Paul F.; Gibson, Steven J.; Murray, Claire E.; Robishaw, Tim; McClure-Griffiths, N. M.; Dickey, John; Pineda, Jorge; Stanimirović, Snežana; Bronfman, L.; Troland, Thomas; PRIMO Collaboration

    2018-03-01

    Hydroxyl (OH) is expected to be abundant in diffuse interstellar molecular gas because it forms along with H2 under similar conditions and forms within a similar extinction range. We have analyzed absorption measurements of OH at 1665 MHz and 1667 MHz toward 44 extragalactic continuum sources, together with the J = 1–0 transitions of 12CO, 13CO, and C18O, and the J = 2–1 transition of 12CO. The excitation temperatures of OH were found to follow a modified lognormal distribution f({T}ex})\\propto \\tfrac{1}{\\sqrt{2π }σ }\\exp ≤ft[-\\tfrac{{[{ln}({T}ex})-{ln}(3.4{{K}})]}2}{2{σ }2}\\right], the peak of which is close to the temperature of the Galactic emission background (CMB+synchrotron). In fact, 90% of the OH has excitation temperatures within 2 K of the Galactic background at the same location, providing a plausible explanation for the apparent difficulty of mapping this abundant molecule in emission. The opacities of OH were found to be small and to peak around 0.01. For gas at intermediate extinctions (AV ∼ 0.05–2 mag), the detection rate of OH with a detection limit N(OH) ≃ 1012 cm‑2 is approximately independent of AV. We conclude that OH is abundant in the diffuse molecular gas and OH absorption is a good tracer of “dark molecular gas (DMG).” The measured fraction of DMG depends on the assumed detection threshold of the CO data set. The next generation of highly sensitive low-frequency radio telescopes, such as FAST and SKA, will make feasible the systematic inventory of diffuse molecular gas through decomposing, in velocity, the molecular (e.g., OH and CH) absorption profiles toward background continuum sources with numbers exceeding what is currently available by orders of magnitude.

  17. Call for papers for special issue of Journal of Molecular Spectroscopy focusing on "Frequency-comb spectroscopy"

    Science.gov (United States)

    Foltynowicz, Aleksandra; Picqué, Nathalie; Ye, Jun

    2018-05-01

    Frequency combs are becoming enabling tools for many applications in science and technology, beyond the original purpose of frequency metrology of simple atoms. The precisely evenly spaced narrow lines of a laser frequency comb inspire intriguing approaches to molecular spectroscopy, designed and implemented by a growing community of scientists. Frequency-comb spectroscopy advances the frontiers of molecular physics across the entire electro-magnetic spectrum. Used as frequency rulers, frequency combs enable absolute frequency measurements and precise line shape studies of molecular transitions, for e.g. tests of fundamental physics and improved determination of fundamental constants. As light sources interrogating the molecular samples, they dramatically improve the resolution, precision, sensitivity and acquisition time of broad spectral-bandwidth spectroscopy and open up new opportunities and applications at the leading edge of molecular spectroscopy and sensing.

  18. Molecular phylogeny of Indo-Pacific carpenter ants (Hymenoptera: Formicidae, Camponotus) reveals waves of dispersal and colonization from diverse source areas

    Czech Academy of Sciences Publication Activity Database

    Clouse, R. M.; Janda, Milan; Blanchard, B.; Sharma, P.; Hoffmann, B. D.; Andersen, A. N.; Czekanski-Moir, J. E.; Krushelnycky, P.; Rabeling, C.; Wilson, E. O.; Economo, E. P.; Sarnat, E. M.; General, D. M.; Alpert, G. D.; Wheeler, W. C.

    2015-01-01

    Roč. 31, č. 4 (2015), s. 424-437 ISSN 0748-3007 R&D Projects: GA ČR GAP505/12/2467 Grant - others:Marie Curie Felloswhip(CZ) PIOFGA2009-25448 Institutional support: RVO:60077344 Keywords : Hymenoptera * Camponotus * molecular phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.952, year: 2015 http://onlinelibrary.wiley.com/doi/10.1111/cla.12099/epdf

  19. Seasonal variation and source estimation of organic compounds in urban aerosol of Augsburg, Germany

    International Nuclear Information System (INIS)

    Pietrogrande, Maria Chiara; Abbaszade, Guelcin; Schnelle-Kreis, Juergen; Bacco, Dimitri; Mercuriali, Mattia; Zimmermann, Ralf

    2011-01-01

    This study reports a general assessment of the organic composition of the PM 2.5 samples collected in the city of Augsburg, Germany in a summer (August-September 2007) and a winter (February-March 2008) campaign of 36 and 30 days, respectively. The samples were directly submitted to in-situ derivatisation thermal desorption gas chromatography coupled with time of flight mass spectrometry (IDTD-GC-TOFMS) to simultaneously determine the concentrations of many classes of molecular markers, such as n-alkanes, iso- and anteiso-alkanes, polycyclic aromatic hydrocarbons (PAHs), oxidized PAHs, n-alkanoic acids, alcohols, saccharides and others. The PCA analysis of the data identified the contributions of three emission sources, i.e., combustion sources, including fossil fuel emissions and biomass burning, vegetative detritus, and oxidized PAHs. The PM chemical composition shows seasonal trend: winter is characterized by high contribution of petroleum/wood combustion while the vegetative component and atmospheric photochemical reactions are predominant in the hot season. - Highlights: → 59 molecular markers were simultaneously determined by thermal desorption GC-MS. → Organic composition of urban PM 2.5 in Augsburg, Germany, was characterized. → Fossil fuel, vegetative detritus, coal/wood burning are the main sources. → Seasonal trends winter vs. summer were identified. - Organic composition of the urban PM 2.5 identifies seasonal trend of the main sources: fossil fuel and biomass combustion sources, vegetative detritus, atmospheric photochemical reactions.

  20. Source apportionment of atmospheric polycyclic aromatic hydrocarbons (PAHs) in Palm Beach County, Florida.

    Science.gov (United States)

    Afshar-Mohajer, Nima; Wilson, Christina; Wu, Chang-Yu; Stormer, James E

    2016-04-01

    Due to concerns about adverse health effects associated with inhalation of atmospheric polycyclic aromatic hydrocarbons (PAHs), 30 ambient air samples were obtained at an air quality monitoring station in Palm Beach County, Florida, from March 2013 to March 2014. The ambient PAH concentration measurements and fractional emission rates of known sources were incorporated into a chemical mass balance model, CMB8.2, developed by EPA, to apportion contributions of three major PAH sources including preharvest sugarcane burning, mobile vehicles, and wildland fires. Strong association between the number of benzene rings and source contribution was found, and mobile vehicles were identified to be the prevailing source (contribution≥56%) for the observed PAHs concentration with lower molecular weights (four or fewer benzene rings) throughout the year. Preharvest sugarcane burning was the primary contributing source for PAHs with relatively higher molecular weights (five or more benzene rings) during the sugarcane burning season (from October to May of the next year). Source contribution of wildland fires varied among PAH compounds but was consistently lower than for sugarcane burning during the sugarcane harvest season. Determining the major sources responsible for ground-level PAHs serves as a tool to improving management strategies for PAH emitting sources and a step toward better protection of the health of residents in terms of exposure to PAHs. The results obtain insight into temporal dominance of PAH polluting sources for those residential areas located near sugarcane burning facilities and have implications beyond Palm Beach County, in areas with high concerns of PAHs and their linked sources. Source apportionment of atmospheric polycyclic hydrocarbons (PAHs) in Palm Beach County, Florida, meant to estimate contributions of major sources in PAH concentrations measured at Belle Glade City of Palm Beach County. Number of benzene rings was found to be the key parameter

  1. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  2. Computational Chemistry and Reaction Engineering Workbench

    Energy Technology Data Exchange (ETDEWEB)

    J. Thomas Mckinnon

    2003-12-19

    The chemical process industries are among the most energy intensive in the US. While much of the energy use cannot be avoided, (e.g., feedstock energy or separations costs), there are tremendous gains to be had through simulation-based optimizations. The heart of any chemical operation is the chemical reactor and it is here that gains can be made either directly (e.g., reduced heat flux) or indirectly (e.g., reduced downstream separations cost due to more efficient reactor design). The objective of this project was to develop an integrated suite of software to facilitate the simulation and optimization of chemical reactors. In the phase of the project supported by this grant, we focused specifically on gas-phase chemical processes such as combustion and pyrolysis.

  3. System of Systems Analytic Workbench - 2017

    Science.gov (United States)

    2017-08-31

    Genetic Algorithm and Particle Swarm Optimization with Type-2 Fuzzy Sets for Generating Systems of Systems Architectures. Procedia Computer Science...The application effort involves modeling an existing messaging network to perform real-time situational awareness. The Analytical Workbench’s

  4. kspectrum: an open-source code for high-resolution molecular absorption spectra production

    International Nuclear Information System (INIS)

    Eymet, V.; Coustet, C.; Piaud, B.

    2016-01-01

    We present the kspectrum, scientific code that produces high-resolution synthetic absorption spectra from public molecular transition parameters databases. This code was originally required by the atmospheric and astrophysics communities, and its evolution is now driven by new scientific projects among the user community. Since it was designed without any optimization that would be specific to any particular application field, its use could also be extended to other domains. kspectrum produces spectral data that can subsequently be used either for high-resolution radiative transfer simulations, or for producing statistic spectral model parameters using additional tools. This is a open project that aims at providing an up-to-date tool that takes advantage of modern computational hardware and recent parallelization libraries. It is currently provided by Méso-Star (http://www.meso-star.com) under the CeCILL license, and benefits from regular updates and improvements. (paper)

  5. Molecular detection of Fasciola hepatica in water sources of District Nowshehra Khyber Pakhtunkhwa Pakistan

    Science.gov (United States)

    Khan, Imran; Khan, Amir Muhammad; Ayaz, Khan, Sanaullah; Anees, Muhammad; Khan, Shaukat Ali

    2012-12-01

    Fascioliasis is spread through contamination of water sources and cause morbidity throughout the world. In the current study 300 water samples were processed by PCR for detection of Fasciola hepatica. The overall prevalence in different water sources was 9.66 % (29/300). Highest prevalence was recorded in drain water16 % (16/100) followed by tube well water 10% (4/40), open well water 8 % (8/100) and the lowest was recorded in tap water 1.66 %(1/60). The significant difference P < 0.05 was recorded during data analysis. The highest prevalence was recorded in summer. It was concluded from the study that cleaning and filtration should be adopted to avoid the health hazards against water borne zoonotic parasites.

  6. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    Science.gov (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  7. Note: A new design for a low-temperature high-intensity helium beam source

    Science.gov (United States)

    Lechner, B. A. J.; Hedgeland, H.; Allison, W.; Ellis, J.; Jardine, A. P.

    2013-02-01

    A high-intensity supersonic beam source is a key component of any atom scattering instrument, affecting the sensitivity and energy resolution of the experiment. We present a new design for a source which can operate at temperatures as low as 11.8 K, corresponding to a beam energy of 2.5 meV. The new source improves the resolution of the Cambridge helium spin-echo spectrometer by a factor of 5.5, thus extending the accessible timescales into the nanosecond range. We describe the design of the new source and discuss experiments characterizing its performance. Spin-echo measurements of benzene/Cu(100) illustrate its merit in the study of a typical slow-moving molecular adsorbate species.

  8. Atomic, molecular, and optical physics electromagnetic radiation

    CERN Document Server

    Dunning, F B; Lucatorto, Thomas

    1997-01-01

    Combined with Volumes 29A and 29B, this volume is a comprehensive treatment of the key experimental methods of atomic, molecular, and optical physics, as well as an excellent experimental handbook for the field. Thewide availability of tunable lasers in the past several years has revolutionized the field and lead to the introduction of many new experimental methods that are covered in these volumes. Traditional methods are also included to ensure that the volumes will be a complete reference source for the field.

  9. Next-generation mid-infrared sources

    Science.gov (United States)

    Jung, D.; Bank, S.; Lee, M. L.; Wasserman, D.

    2017-12-01

    The mid-infrared (mid-IR) is a wavelength range with a variety of technologically vital applications in molecular sensing, security and defense, energy conservation, and potentially in free-space communication. The recent development and rapid commercialization of new coherent mid-infrared sources have spurred significant interest in the development of mid-infrared optical systems for the above applications. However, optical systems designers still do not have the extensive optical infrastructure available to them that exists at shorter wavelengths (for instance, in the visible and near-IR/telecom wavelengths). Even in the field of optoelectronic sources, which has largely driven the growing interest in the mid-infrared, the inherent limitations of state-of-the-art sources and the gaps in spectral coverage offer opportunities for the development of new classes of lasers, light emitting diodes and emitters for a range of potential applications. In this topical review, we will first present an overview of the current state-of-the-art mid-IR sources, in particular thermal emitters, which have long been utilized, and the relatively new quantum- and interband-cascade lasers, as well as the applications served by these sources. Subsequently, we will discuss potential mid-infrared applications and wavelength ranges which are poorly served by the current stable of mid-IR sources, with an emphasis on understanding the fundamental limitations of the current source technology. The bulk of the manuscript will then explore both past and recent developments in mid-infrared source technology, including narrow bandgap quantum well lasers, type-I and type-II quantum dot materials, type-II superlattices, highly mismatched alloys, lead-salts and transition-metal-doped II-VI materials. We will discuss both the advantages and limitations of each of the above material systems, as well as the potential new applications which they might serve. All in all, this topical review does not aim

  10. Emerging Themes in Image Informatics and Molecular Analysis for Digital Pathology.

    Science.gov (United States)

    Bhargava, Rohit; Madabhushi, Anant

    2016-07-11

    Pathology is essential for research in disease and development, as well as for clinical decision making. For more than 100 years, pathology practice has involved analyzing images of stained, thin tissue sections by a trained human using an optical microscope. Technological advances are now driving major changes in this paradigm toward digital pathology (DP). The digital transformation of pathology goes beyond recording, archiving, and retrieving images, providing new computational tools to inform better decision making for precision medicine. First, we discuss some emerging innovations in both computational image analytics and imaging instrumentation in DP. Second, we discuss molecular contrast in pathology. Molecular DP has traditionally been an extension of pathology with molecularly specific dyes. Label-free, spectroscopic images are rapidly emerging as another important information source, and we describe the benefits and potential of this evolution. Third, we describe multimodal DP, which is enabled by computational algorithms and combines the best characteristics of structural and molecular pathology. Finally, we provide examples of application areas in telepathology, education, and precision medicine. We conclude by discussing challenges and emerging opportunities in this area.

  11. Methanol-induced chain termination in poly(3-hydroxybutyrate) biopolymers: molecular weight control

    Science.gov (United States)

    A systematic study was performed to demonstrate the impact of methanol (MeOH) on poly(3-hydroxybutyrate) (PHB) synthesis and molecular weight (MW) control. Glycerine (init. conc. = 1.0%; w/v), was used as the primary carbon source in batch-culture fermentations with varying concentrations (0 to 0.85...

  12. Determination of phosphorus, sulfur and the halogens using high-temperature molecular absorption spectrometry in flames and furnaces-A review

    International Nuclear Information System (INIS)

    Welz, Bernhard; Lepri, Fabio G.; Araujo, Rennan G.O.; Ferreira, Sergio L.C.; Huang Maodong; Okruss, Michael; Becker-Ross, Helmut

    2009-01-01

    The literature about the investigation of molecular spectra of phosphorus, sulfur and the halogens in flames and furnaces, and the use of these spectra for the determination of these non-metals has been reviewed. Most of the investigations were carried out using conventional atomic absorption spectrometers, and there were in essence two different approaches. In the first one, dual-channel spectrometers with a hydrogen or deuterium lamp were used, applying the two-line method for background correction; in the second one, a line source was used that emitted an atomic line, which overlapped with the molecular spectrum. The first approach had the advantage that any spectral interval could be accessed, but it was susceptible to spectral interference; the second one had the advantage that the conventional background correction systems could be used to minimize spectral interferences, but had the problem that an atomic line had to be found, which was overlapping sufficiently well with the maximum of the molecular absorption spectrum. More recently a variety of molecular absorption spectra were investigated using a low-resolution polychromator with a CCD array detector, but no attempt was made to use this approach for quantitative determination of non-metals. The recent introduction and commercial availability of high-resolution continuum source atomic absorption spectrometers is offering completely new possibilities for molecular absorption spectrometry and its use for the determination of non-metals. The use of a high-intensity continuum source together with a high-resolution spectrometer and a CCD array detector makes possible selecting the optimum wavelength for the determination and to exclude most spectral interferences.

  13. Spectroscopy with synchrotron radiation sources: challenges and opportunities

    International Nuclear Information System (INIS)

    Jagatap, B.N.

    2011-01-01

    Spectroscopy and energetics of atoms, molecules and cluster in ultra-violate (UV), vacuum ultra-violate (VUV) and soft X-ray region is one of the frontier topics of research today, These high energy photons allow us to prepare atomic and molecular systems in energy levels far away from their ground levels; the energy region that is characterized by the complex and highly degenerate energy level structure and multiple channels for reaction and energy dissipation. In this talk we provide a bird's eye view of the progress in this area, with a particular emphasis on spectroscopy research using Indian synchrotron sources. We shall also cover the avenues for collaborative research on Indus synchrotron sources, and the challenges and opportunities that await the Indian spectroscopy community

  14. Observations of high-velocity molecular gas near Herbig-Haro objects: HH 24--27 and HH 1--2

    International Nuclear Information System (INIS)

    Snell, R.L.; Edwards, S.

    1982-01-01

    High-velocity CO has been detected in the vicinity of the Herbig-Haro objects HH 24--27. These observations indicate that there are two sources of high-velocity outflow; one centered on an infrared source near HH 26, and the second centered roughly 2' south of HH 24. The redshifted and blueshifted wings in both sources are spatially separated suggesting that the high-velocity gas is due to energetic bipolar outflow from young stars embedded in the molecular cloud. The association of Herbig-Haro objects with regions of high-velocity gas suggests a common origin for both in the interaction of a stellar wind with the ambient molecular cloud. The mass loss rates implied by our observations, assuming that the rate of mass loss has been constant throughout the dynamical lifetime of the bipolar lobes, are roughly 10 -6 M/sub sun/ yr -1 for both sources. We have also searched for high-velocity gas near HH 1--2 but found no evidence for mass outflow in this region

  15. Phylogenetic estimates of diversification rate are affected by molecular rate variation.

    Science.gov (United States)

    Duchêne, D A; Hua, X; Bromham, L

    2017-10-01

    Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  16. Molecular gas in the x-ray bright group NGC 5044 as revealed by ALMA

    Energy Technology Data Exchange (ETDEWEB)

    David, Laurence P.; Forman, William; Vrtilek, Jan; Jones, Christine; O' Sullivan, Ewan [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States); Lim, Jeremy [Department of Physics, University of Hong Kong, Pokfulam Road (Hong Kong); Combes, Francoise [Observatoire de Paris, LERMA, CNRS, 61 Avenue de l' Observatoire, F-75014 Paris (France); Salome, Philippe [LERMA Observatoire de paris, CNRS, 61 rue de l' Observatoire, F-75014 Paris (France); Edge, Alastair; Hamer, Stephen [Institute for Computational Cosmology, Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Sun, Ming [Department of Physics, University of Alabama in Huntsville, Huntsville, AL 35899 (United States); Gastaldello, Fabio; Bardelli, Sandro [INAF - IASF-Milano, Via E. Bassini 15, I-20133 Milano (Italy); Temi, Pasquale [Astrophysics Branch, NASA/Ames Research Center, MS 245-6, Moffett Field, CA 94035 (United States); Schmitt, Henrique [Remote Sensing Division, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375 (United States); Ohyama, Youichi [Academia Sinica, Institute of Astronomy and Astrophysics, Taiwan (China); Mathews, William [University of California Observatories/Lick Observatory, Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Brighenti, Fabrizio [Dipartimento di Astronomia, Universit di Bologna, via Ranzani 1, I-40127 Bologna (Italy); Giacintucci, Simona [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Trung, Dinh-V, E-mail: ldavid@head.cfa.harvard.edu [Institute of Physics, Vietnamese Academy of Science and Technology, 10 DaoTan Street, BaDinh, Hanoi (Viet Nam)

    2014-09-10

    An ALMA observation of the early-type galaxy NGC 5044, which resides at the center of an X-ray bright group with a moderate cooling flow, detected 24 molecular structures within the central 2.5 kpc. The masses of the molecular structures vary from 3 × 10{sup 5} M {sub ☉} to 10{sup 7} M {sub ☉} and the CO(2-1) linewidths vary from 15 to 65 km s{sup –1}. Given the large CO(2-1) linewidths, the observed structures are likely giant molecular associations (GMAs) and not individual giant molecular clouds (GMCs). Only a few of the GMAs are spatially resolved and the average density of these GMAs yields a GMC volume filling factor of about 15%. The masses of the resolved GMAs are insufficient for them to be gravitationally bound, however, the most massive GMA does contain a less massive component with a linewidth of 5.5 km s{sup –1} (typical of an individual virialized GMC). We also show that the GMAs cannot be pressure confined by the hot gas. Given the CO(2-1) linewidths of the GMAs (i.e., the velocity dispersion of the embedded GMCs) they should disperse on a timescale of about 12 Myr. No disk-like molecular structures are detected and all indications suggest that the molecular gas follows ballistic trajectories after condensing out of the thermally unstable hot gas. The 230 GHz luminosity of the central continuum source is 500 times greater than its low frequency radio luminosity and probably reflects a recent accretion event. The spectrum of the central continuum source also exhibits an absorption feature with a linewidth typical of an individual GMC and an infalling velocity of 250 km s{sup –1}.

  17. Determination of bromide in aqueous solutions via the TlBr molecule using high-resolution continuum source graphite furnace molecular absorption spectrometry

    Science.gov (United States)

    Cacho, Frantisek; Machynak, Lubomir; Nemecek, Martin; Beinrohr, Ernest

    2018-06-01

    The paper describes the determination of bromide by evaluating the molecular absorption of thallium mono-bromide (TlBr) at the rotational line at 342.9815 nm by making use a high-resolution continuum source graphite furnace atomic absorption spectrometer. The effects of variables such as the wavelength, graphite furnace program, amount of Tl and the use of a modifier were investigated and optimized. Various chemical modifiers have been studied, such as Pd, Mg, Ag and a mixture of Pd/Mg. It was found that best results were obtained by using Ag which prevents losses of bromide during pyrolysis step through precipitation of bromide as AgBr. In this way, a maximum pyrolysis temperature of 400 °C could be used. The optimum molecule forming temperature was found to be 900 °C. Bromide concentrations in various water samples (CRM, bottled drinking water and tap water) were determined. The quantification was made by both linear calibration and standard addition techniques. The results were matched well those of the reference method. The calibration curve was linear in the range between 1 and 1000 ng Br with a correlation coefficient R = 0.999. The limit of detection and characteristic mass of the method were 0.3 ng and 4.4 ng of Br.

  18. Interstellar medium around supernova remnants associated with gamma-ray sources

    Science.gov (United States)

    Duvidovich, L.; Petriella, A.; Giacani, E.; Dubner, G.

    2017-07-01

    Supernova remnants (SNRs) are potential sources of gamma-rays, either through inverse Compton scattering of electrons off ambient photons or through the decay of neutral pions created by the collision of energetic protons with dense ambient gas. The SNRs G298.6-0.0 and G298.5-0.3 are proposed to be associated to the gamma-ray sources 3FGL J1214.0-6236 and 3FGL J1212.2-6251, respectively. They are located in a complex portion of the Galactic plane, also containing sources of powerful stellar winds such as the star Wolf Rayet HD104994 and the HII regions G298.559-00.114, G298.868-00.432 and G298.228-00.331 with ongoing star formation. We present a study of the neutral hydrogen distribution towards the mentioned SNRs. We found a structure with ellipsoidal morphology that encloses a region containing G298.5-0.3, G298.6-0.0, HD104994, G298.559-00.114 and G298.228-00.331. This HI feature is detected in the velocity range 89-100 km s-1. We propose that the neutral gas would be the accelerated portion (which would explain its high radial velocity) of a gas shell swept up by a series of expansive and explosive events. The rest of this shell (at radial velocities compatible with the systemic velocity of the objects) is not visible because of confusion with galactic emission. We also inspected the distribution of the 12CO gas and found a dense molecular cloud at the systemic velocity of ˜ 22 km s-1 corresponding to the kinematical distance of ˜ 10.4 kpc, compatible with the distance to the SNR G298.6-0.0. This molecular cloud is in spatial coincidence, projected in the sky plane, with the very high energy source associated with the remnant. This fact, suggesting a possible hadronic origin for the gamma-rays emission. Regarding to the SNR G298.5-0.3, smaller and fainter than the previous one, the angular resolution of the molecular data is insufficient to draw meaningful conclusions.

  19. Molecular barcoding, DNA from snake venom, and toxinological research: Considerations and concerns.

    Science.gov (United States)

    Powell, Randy L; Reyes, Steven R; Lannutti, Dominic I

    2006-12-15

    The problem of species identification in toxinological research and solutions such as molecular barcoding and DNA extraction from venom samples are addressed. Molecular barcoding is controversial with both perceived advantages and inherent problems. A method of species identification utilizing mitochondrial DNA from venom has been identified. This method could result in deemphasizing the importance of obtaining detailed information on the venom source prior to analysis. Additional concerns include; a cost prohibitive factor, intraspecific venom variation, and venom processing issues. As researchers demand more stringent records and verification, venom suppliers may be prompted to implement improved methods and controls.

  20. Unveiling the sources of disk heating in spiral galaxies with the CALIFA survey

    NARCIS (Netherlands)

    Pinna, F.; Falcón-Barroso, J.; Martig, M.; van de Ven, G.; Lyubenova, M.; Leaman, R.

    The stellar velocity ellipsoid (SVE) quantifies the amount of velocity dispersion in the vertical, radial and azimuthal directions. Since different disk heating mechanisms (e.g. spiral arms, giant molecular clouds, mergers, etc) affect these components differently, the SVE can constrain the sources

  1. Light and redox switchable molecular components for molecular electronics.

    Science.gov (United States)

    Browne, Wesley R; Feringa, Ben L

    2010-01-01

    The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

  2. 2012 Gordon Research Conference On Molecular And Ionic Clusters

    International Nuclear Information System (INIS)

    McCoy, Anne

    2012-01-01

    The Gordon Research Conference on 'Molecular and Ionic Clusters' focuses on clusters, which are the initial molecular species found in gases when condensation begins to occur. Condensation can take place solely from molecules interacting with each other, mostly at low temperatures, or when molecules condense around charged particles (electrons, protons, metal cations, molecular ions), producing ion molecule clusters. These clusters provide models for solvation, allow a pristine look at geometric as well as electronic structures of molecular complexes or matter in general, their interaction with radiation, their reactivity, their thermodynamic properties and, in particular, the related dynamics. This conference focuses on new ways to make clusters composed of different kinds of molecules, new experimental techniques to investigate the properties of the clusters and new theoretical methods with which to calculate the structures, dynamical motions and energetics of the clusters. Some of the main experimental methods employed include molecular beams, mass spectrometry, laser spectroscopy (from infrared to XUV; in the frequency as well as the time domain) and photoelectron spectroscopy. Techniques include laser absorption spectroscopy, laser induced fluorescence, resonance enhanced photoionization, mass-selected photodissociation, photofragment imaging, ZEKE photoelectron spectroscopy, etc. From the theoretical side, this conference highlights work on potential surfaces and measurable properties of the clusters. The close ties between experiment, theory and computation have been a hallmark of the Gordon Research Conference on Molecular and Ionic Clusters. In the 2012 meeting, we plan to have sessions that will focus on topics including: (1) The use of cluster studies to probe fundamental phenomena; (2) Finite size effects on structure and thermodynamics; (3) Intermolecular forces and cooperative effects; (4) Molecular clusters as models for solvation; and (5) Studies of

  3. An assessment of air as a source of DNA contamination encountered when performing PCR.

    Science.gov (United States)

    Witt, Nina; Rodger, Gillian; Vandesompele, Jo; Benes, Vladimir; Zumla, Alimuddin; Rook, Graham A; Huggett, Jim F

    2009-12-01

    Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as a source of contamination, which might occur during PCR setup, we exposed tubes of water to the air of a laboratory and clean hood for up to 24 h. To increase the chances of contamination, we also investigated a busy open-plan office in the same way. All of the experiments showed the presence of human and rodent DNA contamination. However, there was no accumulation of the contamination in any of the environments investigated, suggesting that the air was not the source of contamination. Even the air from a busy open-plan office was a poor source of contamination for all of the DNA sequences investigated (human, bacterial, fungal, and rodent). This demonstrates that the personnel and immediate laboratory environment are not necessarily to blame for the observed contamination.

  4. Molecular weights distribution and temperature effects in the styrene polymerization initiated with gamma rays

    International Nuclear Information System (INIS)

    Burillo, G.; Martinez, R.

    1979-01-01

    The polymerization of styrene irradiated in a 60 CO source to 18 0 C temperature and to 70 0 C temperature was studied, in order to reduce the irradiation time raising the polymerization rate and looking for a highest molecular weight. The radiation doses used were from 0.2 to 33.26 Mrad, at the rate of 56 rad/sec, the percent of polymerization and the molecular weight formed were determined, the results indicate one highest molecular weight of 132,700 when the radiation dose of 20 Mrad and the temperature of 20 0 C were used, and one of 395,000 when the irradiation is carried out to 70 0 C. (author)

  5. Chirality-dependent friction of bulk molecular solids.

    Science.gov (United States)

    Yang, Dian; Cohen, Adam E

    2014-08-26

    We show that the solid-solid friction between bulk chiral molecular solids can depend on the relative chirality of the two materials. In menthol and 1-phenyl-1-butanol, heterochiral friction is smaller than homochiral friction, while in ibuprofen, heterochiral friction is larger. Chiral asymmetries in the coefficient of sliding friction vary with temperature and can be as large as 30%. In the three compounds tested, the sign of the difference between heterochiral and homochiral friction correlated with the sign of the difference in melting point between racemate (compound or conglomerate) and pure enantiomer. Menthol and ibuprofen each form a stable racemic compound, while 1-phenyl-1-butanol forms a racemic conglomerate. Thus, a difference between heterochiral and homochiral friction does not require the formation of a stable interfacial racemic compound. Measurements of chirality-dependent friction provide a unique means to distinguish the role of short-range intermolecular forces from all other sources of dissipation in the friction of bulk molecular solids.

  6. Molecular epidemiology and evolution of fish Novirhabdoviruses

    Science.gov (United States)

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  7. Atomic and molecular physics with ion storage rings

    International Nuclear Information System (INIS)

    Larsson, M.

    1995-01-01

    Advances in ion-source, accelerator and beam-cooling technology have made it possible to produce high-quality beams of atomic ions in arbitrary charged states as well as molecular and cluster ions are internally cold. Ion beams of low emittance and narrow momentum spread are obtained in a new generation of ion storage-cooler rings dedicated to atomic and molecular physics. The long storage times (∼ 5 s ≤ τ ≤ days) allow the study of very slow processes occurring in charged (positive and negative) atoms, molecules and clusters. Interactions of ions with electrons and/or photons can be studied by merging the stored ion beam with electron and laser beams. The physics of storage rings spans particles having a charge-to-mass ratio ranging from 60 + and C 70 + ) to 0.4 - 1.0 (H + , D + , He 2+ , ..., U 92+ ) and collision processes ranging from <1 meV to ∼ 70 GeV. It incorporates, in addition to atomic and molecular physics, tests of fundamental physics theories and atomic physics bordering on nuclear and chemical physics. This exciting development concerning ion storage rings has taken place within the last five to six years. (author)

  8. Molecular HIV screening.

    Science.gov (United States)

    Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

    2013-09-01

    Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

  9. A SYSTEMATIC SEARCH FOR MOLECULAR OUTFLOWS TOWARD CANDIDATE LOW-LUMINOSITY PROTOSTARS AND VERY LOW LUMINOSITY OBJECTS

    Energy Technology Data Exchange (ETDEWEB)

    Schwarz, Kamber R.; Shirley, Yancy L. [Steward Observatory, 933 N. Cherry Ave., Tucson, AZ 85721 (United States); Dunham, Michael M. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520 (United States)

    2012-10-01

    We present a systematic single-dish search for molecular outflows toward a sample of nine candidate low-luminosity protostars and 30 candidate very low luminosity objects (VeLLOs; L{sub int} {<=} 0.1 L{sub Sun }). The sources are identified using data from the Spitzer Space Telescope cataloged by Dunham et al. toward nearby (D < 400 pc) star-forming regions. Each object was observed in {sup 12}CO and {sup 13}CO J = 2 {yields} 1 simultaneously using the sideband separating ALMA Band-6 prototype receiver on the Heinrich Hertz Telescope at 30'' resolution. Using five-point grid maps, we identify five new potential outflow candidates and make on-the-fly maps of the regions surrounding sources in the dense cores B59, L1148, L1228, and L1165. Of these new outflow candidates, only the map of B59 shows a candidate blue outflow lobe associated with a source in our survey. We also present larger and more sensitive maps of the previously detected L673-7 and the L1251-A-IRS4 outflows and analyze their properties in comparison to other outflows from VeLLOs. The accretion luminosities derived from the outflow properties of the VeLLOs with detected CO outflows are higher than the observed internal luminosity of the protostars, indicating that these sources likely had higher accretion rates in the past. The known L1251-A-IRS3 outflow is detected but not re-mapped. We do not detect clear, unconfused signatures of red and blue molecular wings toward the other 31 sources in the survey indicating that large-scale, distinct outflows are rare toward this sample of candidate protostars. Several potential outflows are confused with the kinematic structure in the surrounding core and cloud. Interferometric imaging is needed to disentangle large-scale molecular cloud kinematics from these potentially weak protostellar outflows.

  10. A SYSTEMATIC SEARCH FOR MOLECULAR OUTFLOWS TOWARD CANDIDATE LOW-LUMINOSITY PROTOSTARS AND VERY LOW LUMINOSITY OBJECTS

    International Nuclear Information System (INIS)

    Schwarz, Kamber R.; Shirley, Yancy L.; Dunham, Michael M.

    2012-01-01

    We present a systematic single-dish search for molecular outflows toward a sample of nine candidate low-luminosity protostars and 30 candidate very low luminosity objects (VeLLOs; L int ≤ 0.1 L ☉ ). The sources are identified using data from the Spitzer Space Telescope cataloged by Dunham et al. toward nearby (D 12 CO and 13 CO J = 2 → 1 simultaneously using the sideband separating ALMA Band-6 prototype receiver on the Heinrich Hertz Telescope at 30'' resolution. Using five-point grid maps, we identify five new potential outflow candidates and make on-the-fly maps of the regions surrounding sources in the dense cores B59, L1148, L1228, and L1165. Of these new outflow candidates, only the map of B59 shows a candidate blue outflow lobe associated with a source in our survey. We also present larger and more sensitive maps of the previously detected L673-7 and the L1251-A-IRS4 outflows and analyze their properties in comparison to other outflows from VeLLOs. The accretion luminosities derived from the outflow properties of the VeLLOs with detected CO outflows are higher than the observed internal luminosity of the protostars, indicating that these sources likely had higher accretion rates in the past. The known L1251-A-IRS3 outflow is detected but not re-mapped. We do not detect clear, unconfused signatures of red and blue molecular wings toward the other 31 sources in the survey indicating that large-scale, distinct outflows are rare toward this sample of candidate protostars. Several potential outflows are confused with the kinematic structure in the surrounding core and cloud. Interferometric imaging is needed to disentangle large-scale molecular cloud kinematics from these potentially weak protostellar outflows.

  11. Versatile Molecular Silver Ink Platform for Printed Flexible Electronics.

    Science.gov (United States)

    Kell, Arnold J; Paquet, Chantal; Mozenson, Olga; Djavani-Tabrizi, Iden; Deore, Bhavana; Liu, Xiangyang; Lopinski, Gregory P; James, Robert; Hettak, Khelifa; Shaker, Jafar; Momciu, Adrian; Ferrigno, Julie; Ferrand, Olivier; Hu, Jian Xiong; Lafrenière, Sylvie; Malenfant, Patrick R L

    2017-05-24

    A silver molecular ink platform formulated for screen, inkjet, and aerosol jet printing is presented. A simple formulation comprising silver neodecanoate, ethyl cellulose, and solvent provides improved performance versus that of established inks, yet with improved economics. Thin, screen-printed traces with exceptional electrical (molecular ink platform enables an aerosol jet-compatible ink that yields conductive features on glass with 2× bulk resistivity and strong adhesion to various plastic substrates. An inkjet formulation is also used to print top source/drain contacts and demonstrate printed high-mobility thin film transistors (TFTs) based on semiconducting single-walled carbon nanotubes. TFTs with mobility values of ∼25 cm 2 V -1 s -1 and current on/off ratios >10 4 were obtained, performance similar to that of evaporated metal contacts in analogous devices.

  12. Hot-cavity studies for the Resonance Ionization Laser Ion Source

    International Nuclear Information System (INIS)

    Henares, J.L.; Lecesne, N.; Hijazi, L.; Bastin, B.; Kron, T.; Lassen, J.; Le Blanc, F.; Leroy, R.; Osmond, B.; Raeder, S.; Schneider, F.; Wendt, K.

    2016-01-01

    The Resonance Ionization Laser Ion Source (RILIS) has emerged as an important technique in many Radioactive Ion Beam (RIB) facilities for its reliability, and ability to ionize target elements efficiently and element selectively. GISELE is an off-line RILIS test bench to study the implementation of an on-line laser ion source at the GANIL separator facility. The aim of this project is to determine the best technical solution which combines high selectivity and ionization efficiency with small ion beam emittance and stable long term operation. The ion source geometry was tested in several configurations in order to find a solution with optimal ionization efficiency and beam emittance. Furthermore, a low work function material was tested to reduce the contaminants and molecular sidebands generated inside the ion source. First results with ZrC ionizer tubes will be presented. Furthermore, a method to measure the energy distribution of the ion beam as a function of the time of flight will be discussed.

  13. A positive (negative) surface ionization source concept for RIB generation

    International Nuclear Information System (INIS)

    Alton, G.D.; Mills, G.D.

    1995-01-01

    A novel, versatile, new concept, spherical-geometry, positive (negative) surface-ionization source has been designed and fabricated which will have the capability of generating both positive- and negative-ion beams without mechanical changes to the source. The source utilizes a highly permeable, high-work-function Ir ionizer (φ∼ = 5.29 eV) for ionizing highly electropositive atoms/molecules; while for negative-surface ionization, the work function is lowered to φ ∼ = 1.43 eV by continually feeding cesium vapor through the ionizer matrix. The use of Cs to effect low work function surfaces for negative ion beam generation has the potential of overcoming the chronic poisoning effects experienced with LaB 6 while enhancing the probability for negative ion formation of atomic and molecular species with low to intermediate electron affinities. The flexibility of operation in either mode makes it especially attractive for RIB applications and, therefore, the source will be used as a complementary replacement for the high-temperature electron impact ionization sources presently in use at the HRIBF The design features and operational principles of the source will be described in this report

  14. The ROSAT Field Sources --- What are they?

    Science.gov (United States)

    Caillault, J.-P.; Briceno, C.; Martin, E. L.; Palla, F.; Wichmann, R.

    Recent studies using the ROSAT All-Sky Survey towards nearby star-forming regions have identified a widely dispersed population of X-ray active stars and have suggested that these objects are older PMS stars located far from molecular clouds. Another group, however, has presented a simple model assuming continuing star formation over the past 10^8 yrs that quantitatively reproduces the number, surface density, X-ray emission, and optical properties of the RASS sources, leading to the argument that these stars are not PMS stars, but young MS stars of ages up to approximately 10^8 yrs. A third party notes that the similarity between molecular cloud lifetimes and the ambipolar diffusion timescale implies that star formation does not take place instantaneously, nor at a constant rate. They thus argue that the probability of finding a large population of old stars in a star-forming region is intrinsically very small and that the post-T Tauri problem is by and large nonexistent.

  15. Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

    OpenAIRE

    Chad A. Stephenson; Miriam Gillett-Kunnath; William A. O’Brien; Robert Kudrawiec; Mark A. Wistey

    2016-01-01

    Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx) offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germyl)methane, or (H3Ge)4C, followed by the design of a hybrid gas/solid-source molecu...

  16. Bibliography of molecular dissociation in heavy particle collisions, 1950--75

    Energy Technology Data Exchange (ETDEWEB)

    McDaniel, E.W.; Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Kirkpatrick, M.I.; Phaneuf, R.A.; Thomas, E.W.

    1979-02-01

    This annotated bibliography lists published work on molecular dissociation in heavy particle collisions for the period 1950 to 1975. Sources include scientific journals, abstract compilations, conference proceedings, books, and reports. The bibliography is arranged alphabetically by author. Each entry indicates whether the work was experimental or theoretical, what energy range was covered, and what reactants were investigated. Following the bibliographical listing are indexes of reactants and authors.

  17. Bibliography of molecular dissociation in heavy particle collisions, 1950--75

    International Nuclear Information System (INIS)

    McDaniel, E.W.; Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Kirkpatrick, M.I.; Phaneuf, R.A.; Thomas, E.W.

    1979-02-01

    This annotated bibliography lists published work on molecular dissociation in heavy particle collisions for the period 1950 to 1975. Sources include scientific journals, abstract compilations, conference proceedings, books, and reports. The bibliography is arranged alphabetically by author. Each entry indicates whether the work was experimental or theoretical, what energy range was covered, and what reactants were investigated. Following the bibliographical listing are indexes of reactants and authors

  18. Thorium molecular negative ion production in a cesium sputter source at BARC-TIFR pelletron accelerator ion source test set up

    International Nuclear Information System (INIS)

    Gupta, A.K.; Mehrotra, N.; Kale, R.M.; Alamelu, D.; Aggarwal, S.K.

    2005-01-01

    Ion source test set up at Pelletron Accelerator facility has been utilized extensively for the production and characterization of negative ions, with particular emphasis being place at the species of experimental users interest. The attention have been focussed towards the formation of rare earth negative ions, due to their importance in the ongoing accelerator mass spectroscopy program and isotopic abundance measurements using secondary negative ion mass spectrometry

  19. Introduction to basic molecular biologic techniques for molecular imaging researches

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2004-01-01

    Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

  20. The use of lasers as sources for Raman spectrometry, resonance Raman spectrometry, and light scattering

    International Nuclear Information System (INIS)

    Capitini, R.; Ceccaldi, M.; Leicknam, J.P.; Plus, R.

    1975-01-01

    The activity of the laboratory is principally centred on the determination of molecular structures and the study of molecular interactions in solution by infrared and Raman spectrometry. With the development of work on relatively large molecules, particularly biological molecules, it became necessary to complete information on the molecular weight and on the intra and intermolecular geometry and interactions of these bodies. In order to obtain these informations Rayleigh scattering and resonance Raman spectrometry were used. The advantages of using vibrational spectrometry, particularly Raman, in conjunction with the diffusion of light for these structural and molecular interaction studies is emphasized. It is shown that these two techniques could not have developed as they have done in the last few years without the use of lasers as light source [fr

  1. Data-mining of potential antitubercular activities from molecular ingredients of traditional Chinese medicines.

    Science.gov (United States)

    Jamal, Salma; Scaria, Vinod

    2014-01-01

    Background. Traditional Chinese medicine encompasses a well established alternate system of medicine based on a broad range of herbal formulations and is practiced extensively in the region for the treatment of a wide variety of diseases. In recent years, several reports describe in depth studies of the molecular ingredients of traditional Chinese medicines on the biological activities including anti-bacterial activities. The availability of a well-curated dataset of molecular ingredients of traditional Chinese medicines and accurate in-silico cheminformatics models for data mining for antitubercular agents and computational filters to prioritize molecules has prompted us to search for potential hits from these datasets. Results. We used a consensus approach to predict molecules with potential antitubercular activities from a large dataset of molecular ingredients of traditional Chinese medicines available in the public domain. We further prioritized 160 molecules based on five computational filters (SMARTSfilter) so as to avoid potentially undesirable molecules. We further examined the molecules for permeability across Mycobacterial cell wall and for potential activities against non-replicating and drug tolerant Mycobacteria. Additional in-depth literature surveys for the reported antitubercular activities of the molecular ingredients and their sources were considered for drawing support to prioritization. Conclusions. Our analysis suggests that datasets of molecular ingredients of traditional Chinese medicines offer a new opportunity to mine for potential biological activities. In this report, we suggest a proof-of-concept methodology to prioritize molecules for further experimental assays using a variety of computational tools. We also additionally suggest that a subset of prioritized molecules could be used for evaluation for tuberculosis due to their additional effect against non-replicating tuberculosis as well as the additional hepato-protection offered by

  2. Mass spectrometric characterization of a pyrolytic radical source using femtosecond ionization

    Energy Technology Data Exchange (ETDEWEB)

    Frey, H M; Beaud, P; Mischler, B; Radi, P P; Tzannis, A P; Gerber, T [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Radicals play, as reactive species, an important role in the chemistry of combustion. In contrast to atmospheric flames where spectra are congested due to high vibrational and rotational excitation, experiments in the cold environment of a molecular beam (MB) yield clean spectra that can be easily attributed to one species by Resonantly Enhanced Multi Photon Ionization (REMP). A pyrolytic radical source has been set up. To characterize the efficiency of the source `soft` ionization with femto second pulses is applied which results in less fragmentation, simplifying the interpretation of the mass spectrum. (author) figs., tabs., refs.

  3. Monitoring the beam flux in molecular beam epitaxy using laser multiphoton ionization

    International Nuclear Information System (INIS)

    Chien, R.; Sogard, M.R.

    1990-01-01

    In this paper, we will describe a method using laser nonresonant multiphoton ionization to measure beam flux in molecular beam epitaxy (MBE) systems. The results were obtained in a test chamber where a focused excimer laser beam was used to photoionize a small fraction of the atomic and molecular beams. The constituents of the beams were identified by a time-of-flight mass spectrometer. Ion signal strength was found to be directly correlated to the temperature of the atomic beam oven. Good stability and sensitivity on gallium, aluminum, and silicon atomic beams was demonstrated. Arsenic was also detected. We demonstrated very sensitive detection of contaminant atomic and molecular constituents of our system. We have also detected the presence of short-term fluctuations in the gallium flux from an effusion source. These fluctuations, previously suspected, can be in excess of ±10%

  4. Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

    Science.gov (United States)

    Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

    2017-06-12

    Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

  5. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study.

    NARCIS (Netherlands)

    van Ingen, Jakko; Kohl, Thomas A; Kranzer, Katharina; Hasse, Barbara; Keller, Peter M; Katarzyna Szafrańska, Anna; Hillemann, Doris; Chand, Meera; Schreiber, Peter Werner; Sommerstein, Rami; Berger, Christoph; Genoni, Michele; Rüegg, Christian; Troillet, Nicolas; Widmer, Andreas F; Becker, Sören L; Herrmann, Mathias; Eckmanns, Tim; Haller, Sebastian; Höller, Christiane; Debast, Sylvia B; Wolfhagen, Maurice J; Hopman, Joost; Kluytmans, Jan; Langelaar, Merel; Notermans, Daan W; Ten Oever, Jaap; van den Barselaar, Peter; Vonk, Alexander B A; Vos, Margreet C; Ahmed, Nada; Brown, Timothy; Crook, Derrick; Lamagni, Theresa; Phin, Nick; Smith, E Grace; Zambon, Maria; Serr, Annerose; Götting, Tim; Ebner, Winfried; Thürmer, Alexander; Utpatel, Christian; Spröer, Cathrin; Bunk, Boyke; Nübel, Ulrich; Bloemberg, Guido V; Böttger, Erik C; Niemann, Stefan; Wagner, Dirk; Sax, Hugo

    2017-01-01

    Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of

  6. Contribution to the study of the molecular scattering of light. Use of a laser as light source (1963); Contribution a l'etude de la diffusion moleculaire de la lumiere. Utilisation d'un laser comme source lumineuse (1963)

    Energy Technology Data Exchange (ETDEWEB)

    Slama, L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1963-07-01

    The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [French] Les experiences sur la diffusion moleculaire de la lumiere ont ete reprises en utilisant un laser a rubis comme source lumineuse. La distribution angulaire de l'intensite diffusee a ete mesuree dans le cas ou le vecteur electrique de l'onde lumineuse incidente est soit dans le plan, soit perpendiculaire a ce plan. Dans le premier cas un bon accord est observe avec la theorie de Rayleigh, ce qui n'est plus vrai dans le second cas. Des sections efficaces differentielles de diffusion ont ete mesurees pour differents gaz. Les valeurs trouvees sont 2 a 3 fois plus grandes que celles prevues par la theorie classique. On a recherche enfin l'effet d'une variation d'intensite du faisceau du laser sur la linearite du phenomene de diffusion. (auteur)

  7. Marine actinomycetes: an ongoing source of novel bioactive metabolites.

    Science.gov (United States)

    Subramani, Ramesh; Aalbersberg, William

    2012-12-20

    Actinomycetes are virtually unlimited sources of novel compounds with many therapeutic applications and hold a prominent position due to their diversity and proven ability to produce novel bioactive compounds. There are more than 22,000 known microbial secondary metabolites, 70% of which are produced by actinomycetes, 20% from fungi, 7% from Bacillus spp. and 1-2% by other bacteria. Among the actinomycetes, streptomycetes group are considered economically important because out of the approximately more than 10,000 known antibiotics, 50-55% are produced by this genus. The ecological role of actinomycetes in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs. The search for and discovery of rare and new actinomycetes is of significant interest to drug discovery due to a growing need for the development of new and potent therapeutic agents. Modern molecular technologies are adding strength to the target-directed search for detection and isolation of bioactive actinomycetes, and continued development of improved cultivation methods and molecular technologies for accessing the marine environment promises to provide access to this significant new source of chemical diversity with novel/rare actinomycetes including new species of previously reported actinomycetes. Copyright © 2012 Elsevier GmbH. All rights reserved.

  8. Infrared images of reflection nebulae and Orion's bar: Fluorescent molecular hydrogen and the 3.3 micron feature

    International Nuclear Information System (INIS)

    Burton, M.G.; Moorhouse, A.; Brand, P.W.J.L.; Roche, P.F.; Geballe, T.R.

    1989-01-01

    Images were obtained of the (fluorescent) molecular hydrogen 1-0 S(1) line, and of the 3.3 micron emission feature, in Orion's Bar and three reflection nebulae. The emission from these species appears to come from the same spatial locations in all sources observed. This suggests that the 3.3 micron feature is excited by the same energetic UV-photons which cause the molecular hydrogen to fluoresce

  9. Molecular Electronic Terms and Molecular Orbital Configurations.

    Science.gov (United States)

    Mazo, R. M.

    1990-01-01

    Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

  10. π Scope: python based scientific workbench with visualization tool for MDSplus data

    Science.gov (United States)

    Shiraiwa, S.

    2014-10-01

    π Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. πScope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on πScope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

  11. Molecular and Recombination Lines in the Central Region of Sagittarius B2

    Science.gov (United States)

    Curtis, J.; Langston, G.

    2005-12-01

    We present observations of recombination and molecular lines towards Sgr B2 in the frequency range 12.4 to 15.0 GHz. In this frequency range, Hα , β , and γ lines, Heα recombination lines and emission from the SO molecule are detected. Molecular absorption lines from OH, H2CO, and CH3CO are detected at velocity 62±3 km/s. Measurements of the line widths and intensities are presented for the central region of Sgr B2. We detect two previously un-reported molecular absorption lines at 12388.0 and 14625.8 MHz (v=0. in LSR Frame). For selected recombination and molecular lines, we present images of a 10x10 arc-minute region centered on Sgr B2(M). We discuss the sources of three H2CO absorption features detected at 62±3, 6±5, and 100±10 km/s. This was done as a summer REU project in 2005 at the National Radio Astronomy Observatory's Green Bank site, and was funded by the National Science Foundation's REU program.

  12. Calcium impurity as a source of non-radiative recombination in (In,Ga)N layers grown by molecular beam epitaxy

    KAUST Repository

    Young, E. C.; Grandjean, N.; Mates, T. E.; Speck, J. S.

    2016-01-01

    Ca as an unintentional impurity has been investigated in III-nitride layers grown by molecular beam epitaxy (MBE). It is found that Ca originates from the substrate surface, even if careful cleaning and rinsing procedures are applied. The initial Ca surface coverage is ∼1012 cm−2, which is consistent with previous reports on GaAs and silicon wafers. At the onset of growth, the Ca species segregates at the growth front while incorporating at low levels. The incorporation rate is strongly temperature dependent. It is about 0.03% at 820 °C and increases by two orders of magnitude when the temperature is reduced to 600 °C, which is the typical growth temperature for InGaN alloy. Consequently, [Ca] is as high as 1018 cm−3 in InGaN/GaN quantum well structures. Such a huge concentration might be detrimental for the efficiency of light emitting diodes (LEDs) if one considers that Ca is potentially a source of Shockley-Read-Hall (SRH) defects. We thus developed a specific growth strategy to reduce [Ca] in the MBE grown LEDs, which consisted of burying Ca in a low temperature InGaN/GaN superlattice (SL) before the growth of the active region. Finally, two LED samples with and without an SL were fabricated. An increase in the output power by one order of magnitude was achieved when Ca was reduced in the LED active region, providing evidence for the role of Ca in the SRH recombination.

  13. Calcium impurity as a source of non-radiative recombination in (In,Ga)N layers grown by molecular beam epitaxy

    KAUST Repository

    Young, E. C.

    2016-11-23

    Ca as an unintentional impurity has been investigated in III-nitride layers grown by molecular beam epitaxy (MBE). It is found that Ca originates from the substrate surface, even if careful cleaning and rinsing procedures are applied. The initial Ca surface coverage is ∼1012 cm−2, which is consistent with previous reports on GaAs and silicon wafers. At the onset of growth, the Ca species segregates at the growth front while incorporating at low levels. The incorporation rate is strongly temperature dependent. It is about 0.03% at 820 °C and increases by two orders of magnitude when the temperature is reduced to 600 °C, which is the typical growth temperature for InGaN alloy. Consequently, [Ca] is as high as 1018 cm−3 in InGaN/GaN quantum well structures. Such a huge concentration might be detrimental for the efficiency of light emitting diodes (LEDs) if one considers that Ca is potentially a source of Shockley-Read-Hall (SRH) defects. We thus developed a specific growth strategy to reduce [Ca] in the MBE grown LEDs, which consisted of burying Ca in a low temperature InGaN/GaN superlattice (SL) before the growth of the active region. Finally, two LED samples with and without an SL were fabricated. An increase in the output power by one order of magnitude was achieved when Ca was reduced in the LED active region, providing evidence for the role of Ca in the SRH recombination.

  14. Characterization of molecular outflows in the substellar domain

    International Nuclear Information System (INIS)

    Phan-Bao, Ngoc; Dang-Duc, Cuong; Lee, Chin-Fei; Ho, Paul T. P.; Li, Di

    2014-01-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M J , which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10 –6 M ☉ to 2.9 × 10 –5 M ☉ and an outflow mass-loss rate from 2.7 × 10 –9 M ☉ yr –1 to 4.1 × 10 –8 M ☉ yr –1 . These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M J in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M J in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  15. Composition and sources of carbonaceous aerosols in Northern Europe during winter

    Science.gov (United States)

    Glasius, M.; Hansen, A. M. K.; Claeys, M.; Henzing, J. S.; Jedynska, A. D.; Kasper-Giebl, A.; Kistler, M.; Kristensen, K.; Martinsson, J.; Maenhaut, W.; Nøjgaard, J. K.; Spindler, G.; Stenström, K. E.; Swietlicki, E.; Szidat, S.; Simpson, D.; Yttri, K. E.

    2018-01-01

    Sources of elemental carbon (EC) and organic carbon (OC) in atmospheric aerosols (carbonaceous aerosols) were investigated by collection of weekly aerosol filter samples at six background sites in Northern Europe (Birkenes, Norway; Vavihill, Sweden; Risoe, Denmark; Cabauw and Rotterdam in The Netherlands; Melpitz, Germany) during winter 2013. Analysis of 14C and a set of molecular tracers were used to constrain the sources of EC and OC. During the four-week campaign, most sites (in particular those in Germany and The Netherlands) were affected by an episode during the first two weeks with high concentrations of aerosol, as continental air masses were transported westward. The analysis results showed a clear, increasing north to south gradient for most molecular tracers. Total carbon (TC = OC + EC) at Birkenes showed an average concentration of 0.5 ± 0.3 μg C m-3, whereas the average concentration at Melpitz was 6.0 ± 4.3 μg C m-3. One weekly mean TC concentration as high as 11 μg C m-3 was observed at Melpitz. Average levoglucosan concentrations varied by an order of magnitude from 25 ± 13 ng m-3 (Birkenes) to 249 ± 13 ng m-3 (Melpitz), while concentrations of tracers of fungal spores (arabitol and mannitol) and vegetative debris (cellulose) were very low, showing a minor influence of primary biological aerosol particles during the North European winter. The fraction of modern carbon generally varied from 0.57 (Melpitz) to 0.91 (Birkenes), showing an opposite trend compared to the molecular tracers and TC. Total concentrations of 10 biogenic and anthropogenic carboxylic acids, mainly of secondary origin, were 4-53 ng m-3, with the lowest concentrations observed at Birkenes and the highest at Melpitz. However, the highest relative concentrations of carboxylic acids (normalized to TC) were observed at the most northern sites. Levels of organosulphates and nitrooxy organosulphates varied more than two orders of magnitude, from 2 to 414 ng m-3, between

  16. Formation of atomic clusters through the laser ablation of refractory materials in a supersonic molecular beam source

    International Nuclear Information System (INIS)

    Haufler, R.E.; Puretzky, A.A.; Compton, R.N.

    1993-01-01

    Concepts which guide the design of atomic cluster supersonic beam sources have been developed. These ideas are founded on the knowledge of laser ablation dynamics and are structured in order to take advantage of certain features of the ablation event. Some of the drawbacks of previous cluster source designs become apparent when the sequence of events following laser ablation are clarified. Key features of the new cluster source design include control of the cluster size distribution, uniform performance with a variety of solid materials and elements, high beam intensity, and significant removal of internal energy during the supersonic expansion

  17. Acceleration of cluster and molecular ions by TIARA 3 MV tandem accelerator

    CERN Document Server

    Saitoh, Y; Tajima, S

    2000-01-01

    We succeeded in accelerating molecular and cluster ions (B sub 2 sub - sub 4 , C sub 2 sub - sub 1 sub 0 , O sub 2 , Al sub 2 sub - sub 4 , Si sub 2 sub - sub 4 , Cu sub 2 sub - sub 3 , Au sub 2 sub - sub 3 , LiF, and AlO) to MeV energies with high-intensity beam currents by means of a 3 MV tandem accelerator in the TIARA facility. These cluster ions were generated by a cesium sputter-type negative ion source. We tested three types of carbon sputter cathodes in which graphite powder was compressed with different pressures. The pressure difference affected the generating ratio of clusters generated to single atom ions extracted from the source and it appeared that the high-density cathode was suitable. We also investigated the optimum gas pressure for charge exchange in the tandem high-voltage terminal. Clusters of larger size tend to require lower pressure than do smaller ones. In addition, we were able to obtain doubly charged AlO molecular ions. (authors)

  18. STATUS REPORT ON DEVELOPMENT OF A HIGH-SPEED HIGH-INTENSITY MOLECULAR BEAM

    Energy Technology Data Exchange (ETDEWEB)

    Knuth, Eldon L.

    1963-07-15

    Status of a high-speed high-intensity molecular beam under development is described. Bases for designs of the several components are presented. Using an arc-heated source and a hypersonic jet, molecular energies exceeding 1 ev and beam intensities of the order of 10/sup 16/ molecules/ cm/sup 2/ sec are anticipated. A two-disk beam chopper and speed selector provides a means for analyzing the speed distribution in the generated beam, for chopping the beam into bursts of nearly monoenergetic molecules suitable for scattering studies using the time-of-flight technique, and for modulating the beam in order to facilitate detection. A through-flow ionization detector possesses the versatility required for scattering studies using the time-of-flight technique. A sorption pump and a turbo pump serve as central components of alternative pumping systems for the collimating chamber. Using the arc-heated source, the converging nozzle, the conduction-radiation-cooled skimmer, the turbo pump (turning at 3400 rpm), the chopperselector (acting only as a chopper), and the detector, an arc-heated beam is generated and detected. (auth)

  19. Progress in Molecular Imaging in Endoscopy and Endomicroscopy for Cancer Imaging

    Directory of Open Access Journals (Sweden)

    Supang Khondee

    2013-01-01

    Full Text Available Imaging is an essential tool for effective cancer management. Endoscopes are important medical instruments for performing in vivo imaging in hollow organs. Early detection of cancer can be achieved with surveillance using endoscopy, and has been shown to reduce mortality and to improve outcomes. Recently, great advancements have been made in endoscopic instruments, including new developments in optical designs, light sources, optical fibers, miniature scanners, and multimodal systems, allowing for improved resolution, greater tissue penetration, and multispectral imaging. In addition, progress has been made in the development of highly-specific optical probes, allowing for improved specificity for molecular targets. Integration of these new endoscopic instruments with molecular probes provides a unique opportunity for significantly improving patient outcomes and has potential to further improve early detection, image guided therapy, targeted therapy, and personalized medicine. This work summarizes current and evolving endoscopic technologies, and provides an overview of various promising optical molecular probes.

  20. Applications of photon-in, photon-out spectroscopy with third-generation, synchrotron-radiation sources

    International Nuclear Information System (INIS)

    Lindle, D.W.; Perera, R.C.C.

    1991-01-01

    This report discusses the following topics: Mother nature's finest test probe; soft x-ray emission spectroscopy with high-brightness synchrotron radiation sources; anisotropy and polarization of x-ray emission from atoms and molecules; valence-hole fluorescence from molecular photoions as a probe of shape-resonance ionization: progress and prospects; structural biophysics on third-generation synchrotron sources; ultra-soft x-ray fluorescence-yield XAFS: an in situ photon-in, photon-out spectroscopy; and x-ray microprobe: an analytical tool for imaging elemental composition and microstructure